1N1H | pdb_00001n1h

Initiation complex of polymerase lambda3 from reovirus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.268 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GH3Click on this verticalbar to view detailsBest fitted CH1Click on this verticalbar to view detailsBest fitted GDPClick on this verticalbar to view detailsBest fitted G7MClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

RNA Synthesis in a Cage--Structural Studies of Reovirus Polymerase [lambda] 3

Tao, Y.Farsetta, D.L.Nibert, M.L.Harrison, S.C.

(2002) Cell 111: 733-745

  • DOI: https://doi.org/10.1016/s0092-8674(02)01110-8
  • Primary Citation of Related Structures:  
    1MUK, 1MWH, 1N1H, 1N35, 1N38

  • PubMed Abstract: 

    The reovirus polymerase and those of other dsRNA viruses function within the confines of a protein capsid to transcribe the tightly packed dsRNA genome segments. The crystal structure of the reovirus polymerase, lambda3, determined at 2.5 A resolution, shows a fingers-palm-thumb core, similar to those of other viral polymerases, surrounded by major N- and C-terminal elaborations, which create a cage-like structure, with four channels leading to the catalytic site. This "caged" polymerase has allowed us to visualize the results of several rounds of RNA polymerization directly in the crystals. A 5' cap binding site on the surface of lambda3 suggests a template retention mechanism by which attachment of the 5' end of the plus-sense strand facilitates insertion of the 3' end of the minus-sense strand into the template channel.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Minor core protein lambda 3B [auth A]1,267Mammalian orthoreovirus 3 DearingMutation(s): 0 
Gene Names: L1
EC: 2.7.7.48
UniProt
Find proteins for P0CK31 (Reovirus type 3 (strain Dearing))
Explore P0CK31 
Go to UniProtKB:  P0CK31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CK31
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GH3
Query on GH3

Download Ideal Coordinates CCD File 
H [auth A]3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
QGYIFQKZZSSUCR-OBXARNEKSA-N
CH1
Query on CH1

Download Ideal Coordinates CCD File 
G [auth A]3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
CHKFLBOLYREYDO-SHYZEUOFSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
F [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
G7M
Query on G7M

Download Ideal Coordinates CCD File 
E [auth A]N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE
C11 H17 N5 O8 P
AOKQNZVJJXPUQA-KQYNXXCUSA-O
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.268 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.883α = 90
b = 85.013β = 90
c = 249.294γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GH3Click on this verticalbar to view detailsBest fitted CH1Click on this verticalbar to view detailsBest fitted GDPClick on this verticalbar to view detailsBest fitted G7MClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description