4RAU | pdb_00004rau

crystal structure of RTOFab in complex with human PF4

• PDB DOI: https://doi.org/10.2210/pdb4RAU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Mus musculus, Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2014-09-11 Released: 2016-03-16 
• Deposition Author(s): Cai, Z., Zhu, Z., Liu, Q., Greene, M.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.74 Å
• R-Value Free: 
  0.284 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Literature

crystal structure of RTOFab in complex with platelet factor 4

Cai, Z., Zhu, Z., Liu, Q., Greene, M.I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 8 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 438.56 kDa 
• Atom Count: 30,074 
• Modeled Residue Count: 3,970 
• Deposited Residue Count: 4,008 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RTOFab light chain	A, D, G, J, M, P, S, V	212	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RTOFab heavy chain	B, E, H, K, N, Q, T, W	219	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet factor 4	C, F, I, L, O, R, U, X	70	Homo sapiens	Mutation(s): 0  Gene Names: PF4, CXCL4, SCYB4
UniProt & NIH Common Fund Data Resources
Find proteins for P02776 (Homo sapiens) Explore P02776  Go to UniProtKB:  P02776
PHAROS:  P02776 GTEx:  ENSG00000163737

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.74 Å
• R-Value Free:  0.284 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.424	α = 90
b = 171.873	β = 90
c = 208.159	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Cai, Z., Zhu, Z., Liu, Q., Greene, M.I.

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary