6K81 | pdb_00006k81

Crystal structure of human VASH1-SVBP complex

• PDB DOI: https://doi.org/10.2210/pdb6K81/pdb

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


• Deposited: 2019-06-11 Released: 2020-02-19 
• Deposition Author(s): Liu, X., Wang, H., Zhang, Y., Feng, Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.242 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Structural insights into tubulin detyrosination by vasohibins-SVBP complex.

Liu, X., Wang, H., Zhu, J., Xie, Y., Liang, X., Chen, Z., Feng, Y., Zhang, Y.

(2019) Cell Discov 5: 65-65

• PubMed: 31908845 
• DOI: https://doi.org/10.1038/s41421-019-0133-7
• Primary Citation Related Structures: 
  6K81

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Organizational Affiliation: 
• 1Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029 China.
2Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Aninal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning 110866 China.
3Tsinghua-Peking Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, 100084 China.
4Max-Planck Partner Group, School of Life Sciences, Tsinghua University, Beijing, 100084 China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.85 kDa 
• Atom Count: 2,316 
• Modeled Residue Count: 274 
• Deposited Residue Count: 431 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulinyl-Tyr carboxypeptidase 1	A	365	Homo sapiens	Mutation(s): 0  Gene Names: VASH1, KIAA1036, VASH EC: 3.4.17.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L8A9 (Homo sapiens) Explore Q7L8A9  Go to UniProtKB:  Q7L8A9
PHAROS:  Q7L8A9 GTEx:  ENSG00000071246

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small vasohibin-binding protein	B	66	Homo sapiens	Mutation(s): 0  Gene Names: SVBP, CCDC23
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N300 (Homo sapiens) Explore Q8N300  Go to UniProtKB:  Q8N300
PHAROS:  Q8N300 GTEx:  ENSG00000177868

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.242 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.452	α = 90
b = 128.995	β = 90
c = 44.54	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Liu, X., Wang, H., Zhang, Y., Feng, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31822012

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references