5JPM

Structure of the complex of human complement C4 with MASP-2 rebuilt using iMDFF

PDB DOI: https://doi.org/10.2210/pdb5JPM/pdb
Entry: 5JPM supersedes: 4FXG

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-05-03 Released: 2016-08-10
Deposition Author(s): Croll, T.I., Andersen, G.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.75 Å
R-Value Free: 0.268
R-Value Work: 0.212
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

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

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4FXG

Macromolecule Content

Total Structure Weight: 468.73 kDa
Atom Count: 32,214
Modelled Residue Count: 4,130
Deposited Residue Count: 4,220
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C4-A	A, D	656	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens) Explore P0C0L4 Go to UniProtKB: P0C0L4
PHAROS: P0C0L4 GTEx: ENSG00000244731
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0L4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C4-A	B, E	767	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens) Explore P0C0L4 Go to UniProtKB: P0C0L4
PHAROS: P0C0L4 GTEx: ENSG00000244731
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0L4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C4-A	C, F	291	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens) Explore P0C0L4 Go to UniProtKB: P0C0L4
PHAROS: P0C0L4 GTEx: ENSG00000244731
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0L4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannan-binding lectin serine protease 2	G, I	154	Homo sapiens	Mutation(s): 2 Gene Names: MASP2 EC: 3.4.21.104
UniProt & NIH Common Fund Data Resources
Find proteins for O00187 (Homo sapiens) Explore O00187 Go to UniProtKB: O00187
PHAROS: O00187 GTEx: ENSG00000009724
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00187
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannan-binding lectin serine protease 2	H, J	242	Homo sapiens	Mutation(s): 1 Gene Names: MASP2 EC: 3.4.21.104
UniProt & NIH Common Fund Data Resources
Find proteins for O00187 (Homo sapiens) Explore O00187 Go to UniProtKB: O00187
PHAROS: O00187 GTEx: ENSG00000009724
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00187
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, L, M, N, O K, L, M, N, O, P	3		N-Glycosylation	Interactions Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Interactions & Density Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	B, E	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.75 Å
R-Value Free: 0.268
R-Value Work: 0.212
R-Value Observed: 0.213
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.01	α = 90
b = 215.01	β = 110.11
c = 142.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Croll, T.I.

Andersen, G.R.

This entry supersedes: 4FXG

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2016-09-14
Changes: Database references
Version 1.2: 2016-09-28
Changes: Database references
Version 1.3: 2019-02-20
Changes: Advisory, Data collection, Derived calculations
Version 1.4: 2019-10-16
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary