6JMR

CD98hc extracellular domain bound to HBJ127 Fab and MEM-108 Fab

PDB DOI: https://doi.org/10.2210/pdb6JMR/pdb
EM Map EMD-9850: EMDB EMDataResource

Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Mus musculus, Homo sapiens
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2019-03-13 Released: 2019-06-19
Deposition Author(s): Lee, Y., Nishizawa, T., Kusakizako, T., Oda, K., Ishitani, R., Yokoyama, T., Nakane, T., Shirouzu, M., Nureki, O.
Funding Organization(s): Japan Society for the Promotion of Science, Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 162.91 kDa
Atom Count: 9,809
Modelled Residue Count: 1,287
Deposited Residue Count: 1,507
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody	A [auth E]	220	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody	B [auth F]	218	Mus musculus	Mutation(s): 0
Entity Groups
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
4F2 cell-surface antigen heavy chain	C [auth B]	631	Homo sapiens	Mutation(s): 0 Gene Names: SLC3A2, MDU1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P08195 (Homo sapiens) Explore P08195 Go to UniProtKB: P08195
PHAROS: P08195 GTEx: ENSG00000168003
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08195
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody	D [auth C]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody	E [auth D]	219	Mus musculus	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: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth A]	2		N-Glycosylation	Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B]	G [auth B], H [auth B], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP16J07405
Japan Agency for Medical Research and Development (AMED)	Japan	JP18am0101082
Japan Agency for Medical Research and Development (AMED)	Japan	JP18am0101115

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary