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), 0.262 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 146.21 kDa 
  • Atom Count: 10,367 
  • Modeled Residue Count: 1,268 
  • Deposited Residue Count: 1,273 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  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
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*AP*UP*UP*AP*GP*C)-3'A [auth B]6N/A
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), 0.262 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.206 (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

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Ligand Structure Quality Assessment 


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