4DKE

Crystal Structure of Human Interleukin-34 Bound to FAb1.1

• PDB DOI: https://doi.org/10.2210/pdb4DKE/pdb

• Classification: CYTOKINE/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni, Cricetulus griseus
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.265 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 141.04 kDa 
• Atom Count: 9,109 
• Modelled Residue Count: 1,156 
• Deposited Residue Count: 1,268 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-34	A, B	190	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
FAb1.1 Heavy Chain	C [auth H], E [auth I]	230	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FAb1.1 Light Chain	D [auth L], F [auth M]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G08748CW GlyCosmos:  G08748CW GlyGen:  G08748CW

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth D]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G26644CA GlyCosmos:  G26644CA GlyGen:  G26644CA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.265 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.549	α = 90
b = 122.465	β = 90
c = 149.155	γ = 90

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., Chen, Y., Stawicki, S., Wu, Y., 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