2J6E

Crystal Structure of an Autoimmune Complex between a Human IgM Rheumatoid Factor and IgG1 Fc reveals a Novel Fc Epitope and Evidence for Affinity Maturation

PDB DOI: https://doi.org/10.2210/pdb2J6E/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Cricetulus griseus, Homo sapiens
Mutation(s): No

Deposited: 2006-09-28 Released: 2007-04-10
Deposition Author(s): Duquerroy, S., Stura, E.A., Bressanelli, S., Browne, H., Beale, D., Hamon, M., Casali, P., Vaney, M.C., Rey, F.A., Sutton, B.J., Taussig, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.288
R-Value Work: 0.223
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

This is version 4.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 156.04 kDa
Atom Count: 10,195
Modelled Residue Count: 1,284
Deposited Residue Count: 1,394
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IG GAMMA-1 CHAIN C REGION	A, B	232	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857 Go to UniProtKB: P01857
PHAROS: P01857 GTEx: ENSG00000211896
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01857
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IGM	C [auth H], D [auth I]	231	Homo sapiens	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IGM	E [auth L], F [auth M]	234	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C], H [auth D]	9		N-Glycosylation	Interactions Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain G [auth C] Focus chain H [auth D]
Glycosylation Resources
GlyTouCan: G19282BU GlyCosmos: G19282BU GlyGen: G19282BU

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain S [auth B] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain V [auth M] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain V [auth M]	L [auth A] M [auth A] N [auth A] R [auth B] S [auth B] L [auth A], M [auth A], N [auth A], R [auth B], S [auth B], V [auth M]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth M] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth M]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B]	J [auth A], Q [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain Q [auth B] Interactions & Density Focus chain J [auth A] Focus chain Q [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain U [auth H] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth H] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A]	O [auth A], P [auth A], T [auth B], U [auth H]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth H] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.288
R-Value Work: 0.223
R-Value Observed: 0.223
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 241.98	α = 90
b = 75.61	β = 91.13
c = 102.4	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-04-10
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-04-03
Changes: Data collection, Derived calculations, Other, Source and taxonomy
Version 1.4: 2019-08-14
Changes: Data collection, Database references, Experimental preparation, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 3.0: 2022-05-04
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 4.0: 2022-05-11
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 4.1: 2023-12-13
Changes: Data collection, Refinement description

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Help and Resources

2J6E

Crystal Structure of an Autoimmune Complex between a Human IgM Rheumatoid Factor and IgG1 Fc reveals a Novel Fc Epitope and Evidence for Affinity Maturation

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

Entity Groups

Sequence Annotations

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Entity ID: 3

Entity Groups

Sequence Annotations

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Entity ID: 4

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)