6ZJG

Crystal structure of ACPA E4 in complex with CII-C-48-CIT

• PDB DOI: https://doi.org/10.2210/pdb6ZJG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-06-29 Released: 2021-07-07 
• Deposition Author(s): Ge, C., Holmdahl, R.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.230 (DCC) 

Starting Model: experimental

Literature

Crystal structure of ACPA E4 in complex with CII-C-48-CIT

Ge, C., Rikard, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 49 kDa 
• Atom Count: 3,361 
• Modelled Residue Count: 437 
• Deposited Residue Count: 455 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CII-C-48-CIT	A [auth B]	18	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACPA E4 Fab fragment - heavy chain	B [auth HHH]	221	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ACPA E4 Fab fragment - light chain	C [auth LLL]	216	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 4
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 [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CIR	A [auth B]	L-PEPTIDE LINKING	C6 H13 N3 O3		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.230 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.183	α = 90
b = 151.774	β = 90
c = 97.066	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Ge, C., Holmdahl, R.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--
Swedish Research Council	Sweden	--

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 2.0: 2022-12-07
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary
• Version 3.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description
• Version 3.1: 2024-01-31
  Changes: Refinement description
• Version 3.2: 2024-10-16
  Changes: Structure summary