10RR | pdb_000010rr

Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Structural Insights into RNA Phosphorylation by the RNase PNK Module of the Human Rixosome Complex.

Gordon, J.Stanley, R.E.

To be published.

Macromolecule Content 

  • Total Structure Weight: 314.3 kDa 
  • Atom Count: 10,366 
  • Modeled Residue Count: 1,368 
  • Deposited Residue Count: 2,770 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal biogenesis protein LAS1L
A, D
777Homo sapiensMutation(s): 3 
Gene Names: LAS1LMSTP060
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4W2 (Homo sapiens)
Explore Q9Y4W2 
Go to UniProtKB:  Q9Y4W2
GTEx:  ENSG00000001497 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4W2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Polynucleotide 5'-hydroxyl-kinase NOL9
B, E
605Homo sapiensMutation(s): 0 
Gene Names: NOL9
EC: 2.7.1.78
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SY16 (Homo sapiens)
Explore Q5SY16 
Go to UniProtKB:  Q5SY16
GTEx:  ENSG00000162408 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SY16
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
CAA RNA
C, F
3Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-26
    Type: Initial release