7Y09

Cryo-EM structure of human IgM-Fc in complex with the J chain and the DBL domain of DBLMSP

PDB DOI: https://doi.org/10.2210/pdb7Y09/pdb
EM Map EMD-33538: EMDB EMDataResource

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

Deposited: 2022-06-03 Released: 2023-03-29
Deposition Author(s): Shen, H., Ji, C., Xiao, J.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.71 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Plasmodium falciparum has evolved multiple mechanisms to hijack human immunoglobulin M

Ji, C., Shen, H., Su, C., Li, Y., Chen, S., Sharp, T.H., Xiao, J.

(2023) Nat Commun 14: 2650

DOI: https://doi.org/10.1038/s41467-023-38320-z

Macromolecule Content

Total Structure Weight: 511.98 kDa
Atom Count: 20,817
Modelled Residue Count: 2,636
Deposited Residue Count: 4,622
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative erythrocyte membrane protein	A [auth R]	656	Plasmodium falciparum	Mutation(s): 0
UniProt
Find proteins for C5HX06 (Plasmodium falciparum) Explore C5HX06 Go to UniProtKB: C5HX06
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5HX06
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin heavy constant mu	B [auth A] C [auth B] D [auth C] E [auth D] F [auth E] B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth K], K [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
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin J chain	L [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
Sequence Annotations Expand
Reference Sequence

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]	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]