7CJB | pdb_00007cjb

VHL recognizes hydroxyproline in RIPK1

• PDB DOI: https://doi.org/10.2210/pdb7CJB/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-09 Released: 2021-07-14 
• Deposition Author(s): Liu, J., Wang, Y., Pan, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

VHL recognizes hydroxyproline in RIPK1

Liu, J., Wang, Y., Pan, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 180.32 kDa 
• Atom Count: 11,190 
• Modeled Residue Count: 1,392 
• Deposited Residue Count: 1,600 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	A, E, I, M	163	Homo sapiens	Mutation(s): 0  Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens) Explore P40337  Go to UniProtKB:  P40337
PHAROS:  P40337 GTEx:  ENSG00000134086

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	B, F, J, N	122	Homo sapiens	Mutation(s): 0  Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370  Go to UniProtKB:  Q15370
PHAROS:  Q15370 GTEx:  ENSG00000103363

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	C, G, K, O	100	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369  Go to UniProtKB:  Q15369
PHAROS:  Q15369 GTEx:  ENSG00000154582

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
THR-LEU-TYR-TYR-MET-ALA-PRO-GLU-HIS-LEU-ASN-ASP-VAL-ASN-ALA	D, H, L, P	15	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens) Explore Q13546  Go to UniProtKB:  Q13546
PHAROS:  Q13546 GTEx:  ENSG00000137275

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	Q [auth E], R [auth I]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	D, H, L, P	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.831	α = 90
b = 94.831	β = 90
c = 361.605	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Liu, J., Wang, Y., Pan, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31500597
National Natural Science Foundation of China (NSFC)	China	21621002

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description