6KXS

Cryo-EM structure of human IgM-Fc in complex with the J chain and the ectodomain of pIgR

PDB DOI: https://doi.org/10.2210/pdb6KXS/pdb
EM Map EMD-0782: EMDB EMDataResource

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

Deposited: 2019-09-12 Released: 2020-02-05
Deposition Author(s): Li, Y., Wang, G., Xiao, J.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Structural insights into immunoglobulin M.

Li, Y., Wang, G., Li, N., Wang, Y., Zhu, Q., Chu, H., Wu, W., Tan, Y., Yu, F., Su, X.D., Gao, N., Xiao, J.

(2020) Science 367: 1014-1017

PubMed: 32029689 Search on PubMed
DOI: https://doi.org/10.1126/science.aaz5425
Primary Citation of Related Structures:
6KXS

PubMed Abstract:
Immunoglobulin M (IgM) plays a pivotal role in both humoral and mucosal immunity. Its assembly and transport depend on the joining chain (J-chain) and the polymeric immunoglobulin receptor (pIgR), but the underlying molecular mechanisms of these processes are unclear. We report a cryo-electron microscopy structure of the Fc region of human IgM in complex with the J-chain and pIgR ectodomain. The IgM-Fc pentamer is formed asymmetrically, resembling a hexagon with a missing triangle. The tailpieces of IgM-Fc pack into an amyloid-like structure to stabilize the pentamer. The J-chain caps the tailpiece assembly and bridges the interaction between IgM-Fc and the polymeric immunoglobulin receptor, which undergoes a large conformational change to engage the IgM-J complex. These results provide a structural basis for the function of IgM.

Organizational Affiliation

State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.

Macromolecule Content

Total Structure Weight: 498.25 kDa
Atom Count: 22,499
Modelled Residue Count: 2,869
Deposited Residue Count: 4,521
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin heavy constant mu	A B C D E A, B, C, D, E, F, G, H, I [auth K], J [auth L]	383	Homo sapiens	Mutation(s): 0 Gene Names: IGHM
UniProt & NIH Common Fund Data Resources
Find proteins for P01871 (Homo sapiens) Explore P01871 Go to UniProtKB: P01871
PHAROS: P01871 GTEx: ENSG00000211899
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01871
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I [auth K] Focus chain J [auth L]	Go to GlyGen: P01871-2
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin J chain	K [auth J]	136	Homo sapiens	Mutation(s): 0 Gene Names: JCHAIN, IGCJ, IGJ
UniProt & NIH Common Fund Data Resources
Find proteins for P01591 (Homo sapiens) Explore P01591 Go to UniProtKB: P01591
PHAROS: P01591 GTEx: ENSG00000132465
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01591
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain K [auth J]	Go to GlyGen: P01591-1
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymeric immunoglobulin receptor	L [auth P]	555	Homo sapiens	Mutation(s): 0 Gene Names: PIGR
UniProt & NIH Common Fund Data Resources
Find proteins for P01833 (Homo sapiens) Explore P01833 Go to UniProtKB: P01833
PHAROS: P01833 GTEx: ENSG00000162896
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01833
Sequence Annotations Expand
Reference Sequence LOADING

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	M [auth I]	2		N-Glycosylation	Interactions Focus chain M [auth I] Interactions & Density Focus chain M [auth I]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain T [auth G] SDF format, chain U [auth H] SDF format, chain V [auth K] SDF format, chain W [auth L] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth G] MOL2 format, chain U [auth H] MOL2 format, chain V [auth K] MOL2 format, chain W [auth L] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F] mmCIF format, chain T [auth G] mmCIF format, chain U [auth H] mmCIF format, chain V [auth K] mmCIF format, chain W [auth L]	N [auth A] O [auth B] P [auth C] Q [auth D] R [auth E] N [auth A], O [auth B], P [auth C], Q [auth D], R [auth E], S [auth F], T [auth G], U [auth H], V [auth K], W [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth K] Focus chain W [auth L] Interactions & Density Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth K] Focus chain W [auth L]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-02-05

Deposition Author(s):

Li, Y.

Wang, G.

Xiao, J.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2020-02-05
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-12-15
Changes: Database references
Version 2.2: 2024-11-20
Changes: Data collection, Structure summary