7NYD

cryoEM structure of 2C9-sMAC

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  mpstruc

  • Deposited: 2021-03-22 Released: 2021-10-06 
  • Deposition Author(s): Menny, A., Couves, E.C., Bubeck, D.
  • Funding Organization(s): European Research Council (ERC), Cancer Research UK, Engineering and Physical Sciences Research Council

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 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



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C8 beta chainA [auth D]537Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07358 (Homo sapiens)
Explore P07358 
Go to UniProtKB:  P07358
PHAROS:  P07358
GTEx:  ENSG00000021852 
Entity Groups  
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UniProt GroupP07358
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C8 alpha chainB [auth E]554Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07357 (Homo sapiens)
Explore P07357 
Go to UniProtKB:  P07357
PHAROS:  P07357
GTEx:  ENSG00000157131 
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UniProt GroupP07357
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C9C [auth G],
F [auth H]
538Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P02748 (Homo sapiens)
Explore P02748 
Go to UniProtKB:  P02748
PHAROS:  P02748
GTEx:  ENSG00000113600 
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UniProt GroupP02748
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C7D [auth C]821Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P10643 (Homo sapiens)
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PHAROS:  P10643
GTEx:  ENSG00000112936 
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UniProt GroupP10643
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C6E [auth B]913Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P13671 (Homo sapiens)
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PHAROS:  P13671
GTEx:  ENSG00000039537 
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UniProt GroupP13671
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C8 gamma chainG [auth F]182Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07360 (Homo sapiens)
Explore P07360 
Go to UniProtKB:  P07360
PHAROS:  P07360
GTEx:  ENSG00000176919 
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UniProt GroupP07360
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C5H [auth A]1,658Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens)
Explore P01031 
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PHAROS:  P01031
GTEx:  ENSG00000106804 
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UniProt GroupP01031
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Oligosaccharides

Help

Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42227JK
GlyCosmos:  G42227JK
GlyGen:  G42227JK
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
R [auth G],
V [auth B],
X [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA
Query on BMA

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L [auth D]
M [auth D]
O [auth E]
P [auth E]
S [auth G]
L [auth D],
M [auth D],
O [auth E],
P [auth E],
S [auth G],
U [auth C]
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
FUC
Query on FUC

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W [auth B]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
CA
Query on CA

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N [auth D],
Q [auth E],
T [auth G],
Y [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTISOLDE
MODEL REFINEMENTCoot9.1
MODEL REFINEMENTREFMAC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionNo. 864751
Cancer Research UKUnited KingdomC24523/A26234
Engineering and Physical Sciences Research CouncilUnited KingdomEP/L015498/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other