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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "recombination/dna"

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Search Summary

This query matches 86 Structures.

Refinements

Structure Determination Methodology

experimental (86)

Scientific Name of Source Organism

	Escherichia coli K-12 (19)
	Escherichia coli (16)
	Danio rerio (15)
	Homo sapiens (13)
	Human spumaretrovirus (13)
	Mus musculus (13)
	synthetic construct (13)
	Punavirus P1 (8)
	Helicoverpa zea (4)
	Saccharomyces cerevisiae (3)

More...

Taxonomy

	Bacteria (41)
	Eukaryota (41)
	Riboviria (13)
	other sequences (13)
	Duplodnaviria (11)
	Archaea (1)

Experimental Method

	X-RAY DIFFRACTION (44)
	ELECTRON MICROSCOPY (42)

Polymer Entity Type

	Protein (86)
	DNA (84)
	RNA (1)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (5)
	2.5 - 3.0 (16)
	3.0 - 3.5 (34)
	3.5 - 4.0 (11)
	4.0 - 4.5 (12)
	> 4.5 (7)

Release Date

	2000 - 2004 (5)
	2005 - 2009 (17)
	2010 - 2014 (16)
	2015 - 2019 (25)
	2020 - 2024 (21)
	2025 - 2029 (2)

Enzyme Classification Name

	Hydrolases (39)
	Transferases (32)
	Ligases (3)

Symmetry Type

	Asymmetric (38)
	Cyclic (41)
	Dihedral (6)
	Helical (4)

SCOP Classification

	All alpha proteins (12)
	Alpha and beta proteins (a+b) (6)
	Alpha and beta proteins (a/b) (7)
	All beta proteins (3)
	Artifacts (2)

AllSelected

1 to 25 of 86 Structures

Page 1 of 4

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1C7Y \| pdb_00001c7y	Download File View File

E.COLI RUVA-HOLLIDAY JUNCTION COMPLEX

Ariyoshi, M., Nishino, T., Iwasaki, H., Shinagawa, H., Morikawa, K.

(2000) Proc Natl Acad Sci U S A 97: 8257-8262

Released	2000-07-21
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Escherichia coli
Macromolecule	Unique protein chains: 1 Unique nucleic acid chains: 8

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1PVP \| pdb_00001pvp	Download File View File

BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, ALSHG BOUND TO THE ENGINEERED RECOGNITION SITE LOXM7

Baldwin, E.P., Martin, S.S., Abel, J., Gelato, K.A., Kim, H., Schultz, P.G., Santoro, S.W.

(2003) Chem Biol 10: 1085-1094

Released	2004-02-17
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Punavirus P1
Macromolecule	Recombinase cre (protein) 34-MER (nucleic acid)

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1PVQ \| pdb_00001pvq	Download File View File

BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, LNSGG BOUND TO THE ENGINEERED RECOGNITION SITE LOXM7

Baldwin, E.P., Martin, S.S., Abel, J., Gelato, K.A., Kim, H., Schultz, P.G., Santoro, S.W.

(2003) Chem Biol 10: 1085-1094

Released	2004-02-17
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Punavirus P1
Macromolecule	Recombinase cre (protein) DNA 34-MER (nucleic acid)

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1PVR \| pdb_00001pvr	Download File View File

BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, LNSGG BOUND TO THE LOXP (WILDTYPE) RECOGNITION SITE

Baldwin, E.P., Martin, S.S., Abel, J., Gelato, K.A., Kim, H., Schultz, P.G., Santoro, S.W.

(2003) Chem Biol 10: 1085-1094

Released	2004-02-17
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Punavirus P1
Macromolecule	Recombinase CRE (protein) 34-MER (nucleic acid)

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1ZR2 \| pdb_00001zr2	Download File View File

Structure of a Synaptic gamma-delta Resolvase Tetramer Covalently Linked to two Cleaved DNAs

Li, W., Kamtekar, S., Xiong, Y., Sarkis, G.J., Grindley, N.D., Steitz, T.A.

(2005) Science 309: 1210-1215

Released	2005-08-30
Method	X-RAY DIFFRACTION 3.9 Å
Organisms	Escherichia coli
Macromolecule	Transposon gamma-delta resolvase (protein) AAA (nucleic acid) TCAGTGTCCGATAATTTAT (nucleic acid) TTATCGGACACTG (nucleic acid)

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1ZR4 \| pdb_00001zr4	Download File View File

Structure of a Synaptic gamma-delta Resolvase Tetramer Covalently linked to two Cleaved DNAs

Li, W., Kamtekar, S., Xiong, Y., Sarkis, G.J., Grindley, N.D., Steitz, T.A.

(2005) Science 309: 1210-1215

Released	2005-08-30
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Escherichia coli
Macromolecule	Transposon gamma-delta resolvase (protein) AAA (nucleic acid) TCAGTGTCCGATAATTTAT (nucleic acid) TTATCGGACACTG (nucleic acid)

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2GM4 \| pdb_00002gm4	Download File View File

An activated, tetrameric gamma-delta resolvase: Hin chimaera bound to cleaved DNA

Kamtekar, S., Ho, R.S., Li, W., Steitz, T.A.

(2006) Proc Natl Acad Sci U S A 103: 10642-10647

Released	2006-06-27
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Escherichia coli
Macromolecule	Transposon gamma-delta resolvase (protein) 5'-D(CPAPGPTPGPTPCPCPGPAPTPAPAPTPTPTPAPTPAPAPA)-3' (nucleic acid) 5'-D(TPTPAPTPCPGPGPAPCPAPCPTPG)-3' (nucleic acid)

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2HOF \| pdb_00002hof	Download File View File

Crystal structure of the pre-cleavage synaptic complex in the cre-loxp site-specific recombination

Ghosh, K., Van Duyne, G.D.

(2007) J Biological Chem 282: 24004-24016

Released	2007-06-26
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Punavirus P1
Macromolecule	Recombinase cre (protein) LoxP DNA (nucleic acid)

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2HOI \| pdb_00002hoi	Download File View File

Crystal structure of the tetrameric pre-cleavage synaptic complex in the cre-loxp site-specific recombination

Ghosh, K., Van Duyne, G.D.

(2007) J Biological Chem 282: 24004-24016

Released	2007-06-26
Method	X-RAY DIFFRACTION 2.601 Å
Organisms	Punavirus P1
Macromolecule	Recombinase Cre (protein) LoxP DNA (nucleic acid)

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2IIE \| pdb_00002iie	Download File View File

single chain Integration Host Factor protein (scIHF2) in complex with DNA

Bao, Q., Droege, P., Davey, C.A.

(2007) J Mol Biology 367: 731-740

Released	2007-02-20
Method	X-RAY DIFFRACTION 2.41 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Integration host factor (protein) DNA (5'-D(DGPDCPDTPDTPDAPDTPDCPDAPDAPDTPDTPDTPDGPDTPDTPDGPDCPDAPDCPDC)-3') (nucleic acid) DNA (5'-D(DGPDGPDCPDCPDAPDAPDAPDAPDAPDAPDGPDCPDAPDTP*DT)-3') (nucleic acid) Phage P H' site (nucleic acid)
Unique Ligands	MN

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2IIF \| pdb_00002iif	Download File View File

single chain Integration Host Factor mutant protein (scIHF2-K45aE) in complex with DNA

Bao, Q., Droege, P., Davey, C.A.

(2007) J Mol Biology 367: 731-740

Released	2007-02-20
Method	X-RAY DIFFRACTION 2.72 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Integration host factor (protein) DNA (5'-D(DGPDCPDTPDTPDAPDTPDCPDAPDAPDTPDTPDTPDGPDTPDTPDGPDCPDAPDCPDC)-3') (nucleic acid) DNA (5'-D(DGPDGPDCPDCPDAPDAPDAPDAPDAPDAPDGPDCPDAPDTP*DT)-3') (nucleic acid) Phage P H' site (nucleic acid)
Unique Ligands	MN

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2R0Q \| pdb_00002r0q	Download File View File

Crystal structure of a serine recombinase- DNA regulatory complex

Rice, P.A., Mouw, K.W.

(2008) Mol Cell 30: 145-155

Released	2008-04-01
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Staphylococcus aureus
Macromolecule	Putative transposon Tn552 DNA-invertase bin3 (protein) 31-MER (nucleic acid)
Unique Ligands	SO4

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3C28 \| pdb_00003c28	Download File View File

Crystal structure of the product synapse complex

Ghosh, K., Van Duyne, G.D.

To be published

Released	2009-02-17
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Escherichia phage P1
Macromolecule	Recombinase cre (protein) LoxP DNA, chain C (nucleic acid) LoxP DNA, chain D (nucleic acid)

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3C29 \| pdb_00003c29	Download File View File

Cre-loxP Synaptic structure

Ghosh, K., Van Duyne, G.D.

To be published

Released	2009-02-17
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia phage P1
Macromolecule	Recombinase cre (protein) LoxP DNA, chain C, (nucleic acid) LoxP DNA, chain D,F (nucleic acid) LoxP DNA, chain E (nucleic acid)

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3CMT \| pdb_00003cmt	Download File View File

Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures

Chen, Z., Yang, H., Pavletich, N.P.

(2008) Nature 453: 489-494

Released	2008-05-20
Method	X-RAY DIFFRACTION 3.15 Å
Organisms	Escherichia coli
Macromolecule	Protein recA (protein) DNA (5'-D(DTPDTPDTPDTPDTPDCPDCPDCPDAPDCPDCPDTPDTPDTPDT)-3') (nucleic acid) DNA (5'-D(PDGPDGPDTPDGPDGP*DG)-3') (nucleic acid)
Unique Ligands	ADP, ALF, MG

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3CMU \| pdb_00003cmu	Download File View File

Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures

Pavletich, N.P.

(2008) Nature 453: 489-494

Released	2008-05-20
Method	X-RAY DIFFRACTION 4.2 Å
Organisms	Escherichia coli
Macromolecule	Protein recA (protein) DNA (5'-D(DTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDT)-3') (nucleic acid)
Unique Ligands	ADP, ALF, MG

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3CMW \| pdb_00003cmw	Download File View File

Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures

Pavletich, N.P.

(2008) Nature 453: 489-494

Released	2008-05-20
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli
Macromolecule	Protein recA (protein) DNA (5'-D(DTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTP*DT)-3') (nucleic acid)
Unique Ligands	ADP, ALF, MG

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3CMX \| pdb_00003cmx	Download File View File

Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures

Pavletich, N.P.

(2008) Nature 453: 489-494

Released	2008-05-20
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Escherichia coli
Macromolecule	Protein recA (protein) DNA (5'-D(DAPDAPDAPDAPDAPDAPDAPDAPDAPDAPDAPDA)-3') (nucleic acid) DNA (5'-D(DTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTPDTP*DT)-3') (nucleic acid)
Unique Ligands	ADP, ALF, MG

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3JBW \| pdb_00003jbw	Download File View File

Cryo-electron microscopy structure of RAG Paired Complex (with NBD, no symmetry)

Ru, H., Chambers, M.G., Fu, T.-M., Tong, A.B., Liao, M., Wu, H.

(2015) Cell 163: 1138-1152

Released	2015-12-09
Method	ELECTRON MICROSCOPY 4.6 Å
Organisms	Danio rerio Homo sapiens
Macromolecule	Unique protein chains: 2 Unique nucleic acid chains: 5
Unique Ligands	ZN

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3JBX \| pdb_00003jbx	Download File View File

Cryo-electron microscopy structure of RAG Signal End Complex (C2 symmetry)

Ru, H., Chambers, M.G., Fu, T.-M., Tong, A.B., Liao, M., Wu, H.

(2015) Cell 163: 1138-1152

Released	2015-12-09
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Danio rerio Homo sapiens
Macromolecule	Unique protein chains: 2 Unique nucleic acid chains: 4
Unique Ligands	MG, ZN

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3JBY \| pdb_00003jby	Download File View File

Cryo-electron microscopy structure of RAG Paired Complex (C2 symmetry)

Ru, H., Chambers, M.G., Fu, T.-M., Tong, A.B., Liao, M., Wu, H.

(2015) Cell 163: 1138-1152

Released	2015-12-09
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Danio rerio Homo sapiens
Macromolecule	V(D)J recombination-activating protein 1 (protein) V(D)J recombination-activating protein 2 (protein) '-D(PGPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3' (nucleic acid) 5'-D(PCPAPCPAPGPTPGPCPTPAPCPAPGPAP*C)-3' (nucleic acid) RSS intermediate reverse strand (nucleic acid)
Unique Ligands	CA, ZN

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3L2Q \| pdb_00003l2q	Download File View File

Crystal structure of the Prototype Foamy Virus (PFV) intasome in apo form

Hare, S., Gupta, S.S., Cherepanov, P.

(2010) Nature 464: 232-236

Released	2010-02-09
Method	X-RAY DIFFRACTION 3.25 Å
Organisms	Human spumaretrovirus
Macromolecule	Integrase (protein) 5'-D(APTPTPGPTPCPAPTPGPGPAPAPTPTPTPTPGPTPA)-3' (nucleic acid) 5'-D(TPAPCPAPAPAPAPTPTPCPCPAPTPGPAPCPA)-3' (nucleic acid)
Unique Ligands	GOL, ZN

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3L2R \| pdb_00003l2r	Download File View File

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium

Hare, S., Gupta, S.S., Cherepanov, P.

(2010) Nature 464: 232-236

Released	2010-02-09
Method	X-RAY DIFFRACTION 2.88 Å
Organisms	Human spumaretrovirus
Macromolecule	Integrase (protein) 5'-D(APTPTPGPTPCPAPTPGPGPAPAPTPTPTPTPGPTPA)-3' (nucleic acid) 5'-D(TPAPCPAPAPAPAPTPTPCPCPAPTPGPAPCPA)-3' (nucleic acid)
Unique Ligands	GOL, MG, NH4, ZN

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3L2U \| pdb_00003l2u	Download File View File

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and GS9137 (Elvitegravir)

Hare, S., Gupta, S.S., Cherepanov, P.

(2010) Nature 464: 232-236

Released	2010-02-09
Method	X-RAY DIFFRACTION 3.15 Å
Organisms	Human spumaretrovirus
Macromolecule	Integrase (protein) 5'-D(APTPTPGPTPCPAPTPGPGPAPAPTPTPTPTPGPTPA)-3' (nucleic acid) 5'-D(TPAPCPAPAPAPAPTPTPCPCPAPTPGPAPCPA)-3' (nucleic acid)
Unique Ligands	ELV, GOL, MG, NH4, ZN

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3L2V \| pdb_00003l2v	Download File View File

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with manganese and MK0518 (Raltegravir)

Hare, S., Gupta, S.S., Cherepanov, P.

(2010) Nature 464: 232-236

Released	2010-02-09
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Human spumaretrovirus
Macromolecule	Integrase (protein) 5'-D(APTPTPGPTPCPAPTPGPGPAPAPTPTPTPTPGPTPA)-3' (nucleic acid) 5'-D(TPAPCPAPAPAPAPTPTPCPCPAPTPGPAPCPA)-3' (nucleic acid)
Unique Ligands	GOL, MN, NH4, RLT, ZN

1 to 25 of 86 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1C7Y | pdb_00001c7y

1PVP | pdb_00001pvp

1PVQ | pdb_00001pvq

1PVR | pdb_00001pvr

1ZR2 | pdb_00001zr2

1ZR4 | pdb_00001zr4

2GM4 | pdb_00002gm4

2HOF | pdb_00002hof

2HOI | pdb_00002hoi

2IIE | pdb_00002iie

2IIF | pdb_00002iif

2R0Q | pdb_00002r0q

3C28 | pdb_00003c28

3C29 | pdb_00003c29

3CMT | pdb_00003cmt

3CMU | pdb_00003cmu

3CMW | pdb_00003cmw

3CMX | pdb_00003cmx

3JBW | pdb_00003jbw

3JBX | pdb_00003jbx

3JBY | pdb_00003jby

3L2Q | pdb_00003l2q

3L2R | pdb_00003l2r

3L2U | pdb_00003l2u

3L2V | pdb_00003l2v