6ION

The complex of C4.4A with its antibody 11H10 Fab fragment

PDB DOI: https://doi.org/10.2210/pdb6ION/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2018-10-30 Released: 2020-01-15
Deposition Author(s): Huang, M.D., Jiang, Y.B., Yuan, C., Lin, L.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.255
R-Value Work: 0.197
R-Value Observed: 0.200

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structures of Human C4.4A Reveal the Unique Association of Ly6/uPAR/alpha-neurotoxin Domain

Jiang, Y.B., Lin, L., Chen, S., Jiang, L.G., Kriegbaum, M.C., Gardsvoll, H., Hansen, L.V., Li, J., Ploug, M., Yuan, C., Huang, M.D.

(2020) Int J Biol Sci 16: 981-993

DOI: https://doi.org/10.7150/ijbs.39919

Macromolecule Content

Total Structure Weight: 69.56 kDa
Atom Count: 4,603
Modelled Residue Count: 606
Deposited Residue Count: 636
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-C4.4A antibody 11H10, light chain	A [auth L]	215	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
anti-C4.4A antibody 11H10, heavy chain	B [auth H]	220	Mus musculus	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
Ly6/PLAUR domain-containing protein 3	C [auth A]	201	Homo sapiens	Mutation(s): 0 Gene Names: C4.4A
UniProt & NIH Common Fund Data Resources
Find proteins for O95274 (Homo sapiens) Explore O95274 Go to UniProtKB: O95274
PHAROS: O95274 GTEx: ENSG00000124466
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95274
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C [auth A]	Go to GlyGen: O95274-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	D [auth B]	2		N-Glycosylation	Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
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 E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.255
R-Value Work: 0.197
R-Value Observed: 0.200
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.86	α = 90
b = 63.96	β = 96.1
c = 107.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31670739
National Natural Science Foundation of China	China	31570745
National Natural Science Foundation of China	China	31370737

Revision History (Full details and data files)

Version 1.0: 2020-01-15
Type: Initial release
Version 1.1: 2020-03-04
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary