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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Fernandez, I."

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Search Summary

This query matches 29 Structures.

Refinements

Structure Determination Methodology

experimental (29)

Scientific Name of Source Organism

	Homo sapiens (9)
	Severe acute respiratory syndrome coronavirus 2 (7)
	Vicugna pacos (5)
	Simian foamy virus (4)
	Brucella abortus str. 2308 A (3)
	Brucella melitensis bv. 1 str. 16M (3)
	Rattus norvegicus (3)
	Androctonus mauritanicus mauritanicus (2)
	Brucella abortus (2)
	Brucella abortus 2308 (1)

More...

Taxonomy

	Eukaryota (16)
	Riboviria (13)
	Bacteria (9)

Experimental Method

	X-RAY DIFFRACTION (21)
	SOLUTION NMR (5)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

Protein (29)

Refinement Resolution (Å)

	1.5 - 2.0 (4)
	2.0 - 2.5 (7)
	2.5 - 3.0 (9)
	3.0 - 3.5 (2)
	3.5 - 4.0 (2)

Release Date

	1995 - 1999 (4)
	2000 - 2004 (1)
	2015 - 2019 (5)
	2020 - 2024 (19)

Enzyme Classification Name

	Transferases (4)
	Hydrolases (3)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (21)
	Cyclic (8)

SCOP Classification

	Alpha and beta proteins (a/b) (2)
	Alpha and beta proteins (a+b) (1)
	All beta proteins (2)
	Small proteins (2)
	All alpha proteins (1)

AllSelected

1 to 25 of 29 Structures

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1BR0 \| pdb_00001br0	Download File View File

THREE DIMENSIONAL STRUCTURE OF THE N-TERMINAL DOMAIN OF SYNTAXIN 1A

Fernandez, I., Ubach, J., Dubulova, I., Zhang, X., Sudhof, T.C., Rizo, J.

(1998) Cell 94: 841-849

Released	1998-09-02
Method	SOLUTION NMR
Organisms	Rattus norvegicus
Macromolecule	PROTEIN (SYNTAXIN 1-A) (protein)

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1BYN \| pdb_00001byn	Download File View File

SOLUTION STRUCTURE OF THE CALCIUM-BOUND FIRST C2-DOMAIN OF SYNAPTOTAGMIN I

Shao, X., Fernandez, I., Sudhof, T.C., Rizo, J.

(1998) Biochemistry 37: 16106-16115

Released	1998-10-21
Method	SOLUTION NMR
Organisms	Rattus norvegicus
Macromolecule	PROTEIN (SYNAPTOTAGMIN I) (protein)
Unique Ligands	CA

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1K5W \| pdb_00001k5w	Download File View File

THREE-DIMENSIONAL STRUCTURE OF THE SYNAPTOTAGMIN 1 C2B-DOMAIN: SYNAPTOTAGMIN 1 AS A PHOSPHOLIPID BINDING MACHINE

Fernandez, I., Arac, D., Ubach, J., Gerber, S.H., Shin, O., Gao, Y., Anderson, R.G.W., Sudhof, T.C., Rizo, J.

(2001) Neuron 32: 1057-1069

Released	2002-01-23
Method	SOLUTION NMR
Organisms	Rattus norvegicus
Macromolecule	Synaptotagmin I (protein)
Unique Ligands	CA

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1KTX \| pdb_00001ktx	Download File View File

KALIOTOXIN (1-37) SHOWS STRUCTURAL DIFFERENCES WITH RELATED POTASSIUM CHANNEL BLOCKERS

Fernandez, I., Romi, R., Szendefi, S., Martin-Eauclaire, M.-F., Rochat, H., Van Rietschtoten, J., Pons, M., Giralt, E.

(1994) Biochemistry 33: 14256-14263

Released	1995-01-26
Method	SOLUTION NMR
Organisms	Androctonus mauritanicus mauritanicus
Macromolecule	KALIOTOXIN (protein)

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2KTX \| pdb_00002ktx	Download File View File

COMPLETE KALIOTOXIN FROM ANDROCTONUS MAURETANICUS MAURETANICUS, NMR, 18 STRUCTURES

Gairi, M., Romi, R., Fernandez, I., Rochat, H., Martin-Eauclaire, M.-F., Van Rietschtoten, J., Pons, M., Giralt, E.

(1997) J Pept Sci 3: 314-319

Released	1997-06-16
Method	SOLUTION NMR
Organisms	Androctonus mauritanicus mauritanicus
Macromolecule	KALIOTOXIN (protein)

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4D6X \| pdb_00004d6x	Download File View File

Crystal structure of the receiver domain of NtrX from Brucella abortus

Klinke, S., Fernandez, I., Carrica, M.C., Otero, L.H., Goldbaum, F.A.

(2015) J Mol Biology 427: 3258

Released	2015-07-08
Method	X-RAY DIFFRACTION 2.11 Å
Organisms	Brucella abortus
Macromolecule	BACTERIAL REGULATORY, FIS FAMILY PROTEIN (protein)
Unique Ligands	IMD

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4D6Y \| pdb_00004d6y	Download File View File

Crystal structure of the receiver domain of NtrX from Brucella abortus in complex with beryllofluoride and magnesium

Otero, L.H., Fernandez, I., Carrica, M.C., Klinke, S., Goldbaum, F.A.

(2015) J Mol Biology 427: 3258

Released	2015-07-08
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Brucella abortus
Macromolecule	BACTERIAL REGULATORY, FIS FAMILY PROTEIN (protein)
Unique Ligands	BEF, MG

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5M7N \| pdb_00005m7n	Download File View File

Crystal structure of NtrX from Brucella abortus in complex with ATP processed with the CrystalDirect automated mounting and cryo-cooling technology

Cornaciu, I., Fernandez, I., Hoffmann, G., Carrica, M.C., Goldbaum, F.A., Marquez, J.A.

(2017) J Mol Biology 429: 1192-1212

Released	2017-01-25
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Brucella abortus str. 2308 A
Macromolecule	Nitrogen assimilation regulatory protein (protein)
Unique Ligands	ATP, MG

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5M7O \| pdb_00005m7o	Download File View File

Crystal structure of NtrX from Brucella abortus processed with the CrystalDirect automated mounting and cryo-cooling technology

Cornaciu, I., Fernandez, I., Hoffmann, G., Carrica, M.C., Goldbaum, F.A., Marquez, J.A.

(2017) J Mol Biology 429: 1192-1212

Released	2017-01-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Brucella abortus str. 2308 A
Macromolecule	Nitrogen assimilation regulatory protein (protein)
Unique Ligands	MG

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5M7P \| pdb_00005m7p	Download File View File

Crystal structure of NtrX from Brucella abortus in complex with ADP processed with the CrystalDirect automated mounting and cryo-cooling technology

Cornaciu, I., Fernandez, I., Hoffmann, G., Carrica, M.C., Goldbaum, F.A., Marquez, J.A.

(2017) J Mol Biology 429: 1192-1212

Released	2017-01-25
Method	X-RAY DIFFRACTION 2.36 Å
Organisms	Brucella abortus str. 2308 A
Macromolecule	Nitrogen assimilation regulatory protein (protein)
Unique Ligands	ADP, MG

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6PH2 \| pdb_00006ph2	Download File View File

Complete LOV domain from the LOV-HK sensory protein from Brucella abortus (mutant C69S, construct 15-155)

Rinaldi, J., Otero, L.H., Fernandez, I., Goldbaum, F.A., Shin, H., Yang, X., Klinke, S.

(2021) mBio 12:

Released	2020-12-30
Method	X-RAY DIFFRACTION 2.34 Å
Organisms	Brucella melitensis bv. 1 str. 16M
Macromolecule	Blue-light-activated histidine kinase (protein)
Unique Ligands	FMN

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6PH3 \| pdb_00006ph3	Download File View File

LOV-PAS construct from the LOV-HK sensory protein from Brucella abortus (dark-adapted, construct 15-273)

Rinaldi, J., Otero, L.H., Fernandez, I., Goldbaum, F.A., Shin, H., Yang, X., Klinke, S.

(2021) mBio 12:

Released	2020-12-30
Method	X-RAY DIFFRACTION 2.74 Å
Organisms	Brucella melitensis bv. 1 str. 16M
Macromolecule	Blue-light-activated histidine kinase (protein)
Unique Ligands	FMN

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6PH4 \| pdb_00006ph4	Download File View File

Full length LOV-PAS-HK construct from the LOV-HK sensory protein from Brucella abortus (light-adapted, construct 15-489)

Rinaldi, J., Otero, L.H., Fernandez, I., Goldbaum, F.A., Shin, H., Yang, X., Klinke, S.

(2021) mBio 12:

Released	2020-12-30
Method	X-RAY DIFFRACTION 3.25 Å
Organisms	Brucella melitensis bv. 1 str. 16M
Macromolecule	Blue-light-activated histidine kinase (protein)
Unique Ligands	ACP, CL, FMN, MG

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6PPS \| pdb_00006pps	Download File View File

A blue light illuminated LOV-PAS construct from the LOV-HK sensory protein from Brucella abortus (construct 15-273)

Rinaldi, J., Fernandez, I., Shin, H., Gunawardana, S., Otero, L.H., Cerutti, M.L., Yang, X., Klinke, S., Goldbaum, F.A.

(2021) mBio 12:

Released	2020-07-15
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Brucella abortus 2308
Macromolecule	Blue-light-activated histidine kinase (protein)
Unique Ligands	FMN

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7PC2 \| pdb_00007pc2	Download File View File

HIV-1 Env (BG505 SOSIP.664) in complex with the IgA bNAb 7-269 and the antibody 3BNC117.

Fernandez, I., Bontems, F., Pehau-Arnaudet, G., Rey, F.

(2022) J Exp Medicine 219:

Released	2022-02-23
Method	ELECTRON MICROSCOPY 2.8 Å
Organisms	Homo sapiens Human immunodeficiency virus
Macromolecule	Unique protein chains: 6
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

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7Q3Q \| pdb_00007q3q	Download File View File

Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobody VHH-12

Fernandez, I., Pederzoli, R., Rey, F.A.

To be published

Released	2022-11-16
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Severe acute respiratory syndrome coronavirus 2 Vicugna pacos
Macromolecule	Spike glycoprotein (protein) VHH-12 (protein)
Unique Ligands	CL, GOL, SO4
Unique branched monosaccharides	NAG

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7Q3R \| pdb_00007q3r	Download File View File

Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobodies VHH-F04 and VHH-G09

Fernandez, I., Pederzoli, R., Rey, F.A.

To be published

Released	2022-11-16
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Severe acute respiratory syndrome coronavirus 2 Vicugna pacos
Macromolecule	Spike glycoprotein (protein) VHH-F04 (protein) VHH-G09 (protein)
Unique Ligands	CL
Unique branched monosaccharides	NAG

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7QEZ \| pdb_00007qez	Download File View File

Crystal structure of the SARS-CoV-2 RBD in complex with the ultrapotent antibody CV2.1169 and CR3022

Fernandez, I., Rey, F.A.

(2022) J Exp Medicine 219:

Released	2022-05-18
Method	X-RAY DIFFRACTION 2.89 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	CR3022 heavy chain (protein) CR3022 light chain (protein) CV2.1169 IgA heavy chain (protein) CV2.1169 light chain (protein) Spike protein S1 (protein)
Unique Ligands	NAG, SO4

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7QF0 \| pdb_00007qf0	Download File View File

Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.2325

Fernandez, I., Pederzoli, R., Rey, F.A.

(2022) J Exp Medicine 219:

Released	2022-05-18
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	CV2.2325 heavy chain (protein) CV2.2325 light chain (protein) Spike protein S1 (protein)
Unique Ligands	CL, NA
Unique branched monosaccharides	NAG

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7QF1 \| pdb_00007qf1	Download File View File

Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.6264

Fernandez, I., Pederzoli, R., Rey, F.A.

(2022) J Exp Medicine 219:

Released	2022-05-18
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	CV2.6264 heavy chain (protein) CV2.6264 light chain (protein) Spike protein S1 (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, NAG

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8AEZ \| pdb_00008aez	Download File View File

X-ray structure of the deglycosylated receptor binding domain of Env glycoprotein of Simian Foamy virus

Backovic, M.

(2023) Nat Commun 14: 1262-1262

Released	2023-02-22
Method	X-RAY DIFFRACTION 2.574 Å
Organisms	Simian foamy virus
Macromolecule	Envelope glycoprotein gp130 (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

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8AIC \| pdb_00008aic	Download File View File

X-ray structure of the receptor binding domain of Env glycoprotein of Simian Foamy virus

Backovic, M., Fernandez, I.

(2023) Nat Commun 14: 1262-1262

Released	2023-02-22
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Simian foamy virus
Macromolecule	Envelope glycoprotein gp130 (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

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8QH0 \| pdb_00008qh0	Download File View File

Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194

Fernandez, I., Rey, F.A.

To be published

Released	2024-06-19
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Cv2.3194 Heavy chain (protein) IGK@ protein (protein) Spike protein S1 (protein)
Unique Ligands	GOL, PRO
Unique branched monosaccharides	NAG

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8QH1 \| pdb_00008qh1	Download File View File

Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody Cv2.3194

Fernandez, I., Rey, F.A.

To be published

Released	2024-06-19
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Cv2.3194 heavy chain (protein) IGK@ protein (protein) Spike glycoprotein (protein)
Unique Ligands	NAG

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8RM0 \| pdb_00008rm0	Download File View File

Cryo-EM structure of a Foamy Virus fusion glycoprotein stabilized in the prefusion conformation

Fernandez, I., Backovic, M.

(2024) Sci Adv 10: eado7035-eado7035

Released	2024-10-23
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Simian foamy virus
Macromolecule	Envelope glycoprotein gp130 (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

1 to 25 of 29 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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1BR0 | pdb_00001br0

1BYN | pdb_00001byn

1K5W | pdb_00001k5w

1KTX | pdb_00001ktx

2KTX | pdb_00002ktx

4D6X | pdb_00004d6x

4D6Y | pdb_00004d6y

5M7N | pdb_00005m7n

5M7O | pdb_00005m7o

5M7P | pdb_00005m7p

6PH2 | pdb_00006ph2

6PH3 | pdb_00006ph3

6PH4 | pdb_00006ph4

6PPS | pdb_00006pps

7PC2 | pdb_00007pc2

7Q3Q | pdb_00007q3q

7Q3R | pdb_00007q3r

7QEZ | pdb_00007qez

7QF0 | pdb_00007qf0

7QF1 | pdb_00007qf1

8AEZ | pdb_00008aez

8AIC | pdb_00008aic

8QH0 | pdb_00008qh0

8QH1 | pdb_00008qh1

8RM0 | pdb_00008rm0