4DKD

Crystal Structure of Human Interleukin-34 Bound to Human CSF-1R

• PDB DOI: https://doi.org/10.2210/pdb4DKD/pdb

• Classification: CYTOKINE/TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2012-02-03 Released: 2012-04-11 
• Deposition Author(s): Ma, X., Bazan, J.F., Starovasnik, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.287 
• R-Value Work: 0.252 
• R-Value Observed: 0.254 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77.01 kDa 
• Atom Count: 4,872 
• Modelled Residue Count: 593 
• Deposited Residue Count: 662 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-34	A, B	185	Homo sapiens	Mutation(s): 0  Gene Names: IL34, C16orf77
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZMJ4 (Homo sapiens) Explore Q6ZMJ4  Go to UniProtKB:  Q6ZMJ4
PHAROS:  Q6ZMJ4 GTEx:  ENSG00000157368

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage colony-stimulating factor 1 receptor	C	292	Homo sapiens	Mutation(s): 0  Gene Names: CSF1R, FMS EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07333 (Homo sapiens) Explore P07333  Go to UniProtKB:  P07333
PHAROS:  P07333 GTEx:  ENSG00000182578

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth C], I [auth C], J [auth C], K [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA	F [auth A], G [auth B]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.287 
• R-Value Work: 0.252 
• R-Value Observed: 0.254 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.361	α = 90
b = 101.361	β = 90
c = 175.252	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Ma, X., Bazan, J.F., Starovasnik, M.A.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary