6A6L | pdb_00006a6l

Crystal structure of the cold shock domain of YB-1 in complex with m5C RNA

PDB DOI: https://doi.org/10.2210/pdb6A6L/pdb
NAKB: 6A6L

Classification: RNA BINDING PROTEIN/RNA
Organism(s): Homo sapiens
Expression System: Escherichia coli, synthetic construct
Mutation(s): No

Deposited: 2018-06-28 Released: 2019-06-19
Deposition Author(s): Huang, Y.
Funding Organization(s): National Natural Science Foundation of China, Chinese Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.207 (Depositor), 0.230 (DCC)
R-Value Work:
0.180 (Depositor)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the cold shock domain of YB-1 in complex with m5C RNA

Huang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 10.82 kDa
Atom Count: 734
Modeled Residue Count: 80
Deposited Residue Count: 89
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease-sensitive element-binding protein 1	A	83	Homo sapiens	Mutation(s): 0 Gene Names: YB1
UniProt & NIH Common Fund Data Resources
Find proteins for P67809 (Homo sapiens) Explore P67809 Go to UniProtKB: P67809
PHAROS: P67809 GTEx: ENSG00000065978
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P67809
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (5'-R(PCPAPUP(5MC))-3')	B [auth D]	6	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.207 (Depositor), 0.230 (DCC)
R-Value Work: 0.180 (Depositor)
R-Value Observed: 0.183 (Depositor)

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.38	α = 90
b = 66.38	β = 90
c = 34.702	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	91640102
Chinese Academy of Sciences	China	XDB08010202

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.