6GY4 | pdb_00006gy4

Crystal structure of the N-terminal KH domain of human BICC1

• PDB DOI: https://doi.org/10.2210/pdb6GY4/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-28 Released: 2018-07-18 
• Deposition Author(s): Newman, J.A., Katis, V.L., Shrestha, L., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.303 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the N-terminal KH domain of human BICC1

Newman, J.A., Katis, V.L., Shrestha, L., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.84 kDa 
• Atom Count: 2,310 
• Modeled Residue Count: 293 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein bicaudal C homolog 1	A, B, C, D	86	Homo sapiens	Mutation(s): 0  Gene Names: BICC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H694 (Homo sapiens) Explore Q9H694  Go to UniProtKB:  Q9H694
PHAROS:  Q9H694 GTEx:  ENSG00000122870

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XPE	H [auth C]	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL C20 H42 O11 DTPCFIHYWYONMD-UHFFFAOYSA-N
SO4	E [auth B], F [auth C], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.303 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.406	α = 90
b = 153.164	β = 90
c = 86.235	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-18 
Deposition Author(s): Newman, J.A., Katis, V.L., Shrestha, L., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2018-07-18
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description