6ZJG | pdb_00006zjg

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.265 (Depositor), 0.264 (DCC)
R-Value Work:
0.223 (Depositor), 0.223 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 3.2 of the entry. See complete history.

Literature

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

Ge, C., Rikard, H.

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by: Sequence | 3D Structure

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

Find similar proteins by:

| 3D Structure

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

Find similar proteins by:

| 3D Structure

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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	2		N-Glycosylation	Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CIR Query on 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), 0.264 (DCC)
R-Value Work: 0.223 (Depositor), 0.223 (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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-07

Deposition Author(s):

Ge, C.

Holmdahl, R.

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

Revision History (Full details and data files)

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