7WLD

Cryo-EM structure of the human glycosylphosphatidylinositol transamidase complex at 2.53 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular insights into biogenesis of glycosylphosphatidylinositol anchor proteins.

Xu, Y.Jia, G.Li, T.Zhou, Z.Luo, Y.Chao, Y.Bao, J.Su, Z.Qu, Q.Li, D.

(2022) Nat Commun 13: 2617-2617

  • DOI: https://doi.org/10.1038/s41467-022-30250-6
  • Primary Citation of Related Structures:  
    7WLD

  • PubMed Abstract: 

    Eukaryotic cells are coated with an abundance of glycosylphosphatidylinositol anchor proteins (GPI-APs) that play crucial roles in fertilization, neurogenesis, and immunity. The removal of a hydrophobic signal peptide and covalent attachment of GPI at the new carboxyl terminus are catalyzed by an endoplasmic reticulum membrane GPI transamidase complex (GPI-T) conserved among all eukaryotes. Here, we report the cryo-electron microscopy (cryo-EM) structure of the human GPI-T at a global 2.53-Å resolution, revealing an equimolar heteropentameric assembly. Structure-based mutagenesis suggests a legumain-like mechanism for the recognition and cleavage of proprotein substrates, and an endogenous GPI in the structure defines a composite cavity for the lipid substrate. This elongated active site, stemming from the membrane and spanning an additional ~22-Å space toward the catalytic dyad, is structurally suited for both substrates which feature an amphipathic pattern that matches this geometry. Our work presents an important step towards the mechanistic understanding of GPI-AP biosynthesis.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of CAS, Chinese Academy of Sciences (CAS), 320 Yueyang Road, 200030, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosylphosphatidylinositol anchor attachment 1 proteinA [auth G]886Homo sapiensMutation(s): 0 
Gene Names: GPAA1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O43292 (Homo sapiens)
Explore O43292 
Go to UniProtKB:  O43292
PHAROS:  O43292
GTEx:  ENSG00000197858 
Entity Groups  
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UniProt GroupO43292
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GPI-anchor transamidaseB [auth K]647Homo sapiensMutation(s): 0 
Gene Names: PIGK
EC: 3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92643 (Homo sapiens)
Explore Q92643 
Go to UniProtKB:  Q92643
PHAROS:  Q92643
GTEx:  ENSG00000142892 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92643
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GPI transamidase component PIG-SC [auth S]816Homo sapiensMutation(s): 0 
Gene Names: PIGS
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96S52 (Homo sapiens)
Explore Q96S52 
Go to UniProtKB:  Q96S52
PHAROS:  Q96S52
GTEx:  ENSG00000087111 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96S52
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
GPI transamidase component PIG-TD [auth T]831Homo sapiensMutation(s): 0 
Gene Names: PIGT
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q969N2 (Homo sapiens)
Explore Q969N2 
Go to UniProtKB:  Q969N2
PHAROS:  Q969N2
GTEx:  ENSG00000124155 
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UniProt GroupQ969N2
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol glycan anchor biosynthesis class U proteinE [auth U]712Homo sapiensMutation(s): 0 
Gene Names: PIGU
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H490 (Homo sapiens)
Explore Q9H490 
Go to UniProtKB:  Q9H490
PHAROS:  Q9H490
GTEx:  ENSG00000101464 
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UniProt GroupQ9H490
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth A]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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Y [auth U]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
AJP
Query on AJP

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I [auth G]Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
06O (Subject of Investigation/LOI)
Query on 06O

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GA [auth U][(2~{R})-1-hexadecanoyloxy-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-propan-2-yl] (9~{Z},11~{Z})-octadeca-9,11-dienoate
C59 H109 O14 P
LFLYMSDVBHTFNN-ZDYRQTLBSA-N
P5S
Query on P5S

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Q [auth K]O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
BJR
Query on BJR

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J [auth G],
K [auth G]
(4S,7R)-7-[(hexadecanoyloxy)methyl]-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-3,5,8-trioxa-4lambda~5~-phosphahexacosan-1-aminium
C42 H85 N O8 P
PZNPLUBHRSSFHT-RRHRGVEJSA-O
PEE
Query on PEE

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L [auth G]1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
DKB
Query on DKB

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CA [auth U][(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate
C39 H78 N O8 P
RPJZYOHZALDGKI-DIPNUNPCSA-N
Y01
Query on Y01

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DA [auth U]
EA [auth U]
FA [auth U]
G
H [auth G]
DA [auth U],
EA [auth U],
FA [auth U],
G,
H [auth G],
M [auth G],
N [auth G],
O [auth G],
Z [auth U]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
CLR
Query on CLR

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AA [auth U],
BA [auth U],
S,
T [auth S],
U [auth S]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
05E (Subject of Investigation/LOI)
Query on 05E

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V [auth T]2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate
C8 H18 N O9 P
AMJFTSXJOORFJX-HEIBUPTGSA-N
NAG
Query on NAG

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R [auth S],
W [auth T]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PA1 (Subject of Investigation/LOI)
Query on PA1

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X [auth T]2-amino-2-deoxy-alpha-D-glucopyranose
C6 H13 N O5
MSWZFWKMSRAUBD-UKFBFLRUSA-N
CA
Query on CA

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P [auth K]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82151215
National Natural Science Foundation of China (NSFC)China31870726
National Natural Science Foundation of China (NSFC)China82041016
National Natural Science Foundation of China (NSFC)China32070049
Ministry of Science and Technology (MoST, China)China2021YFA1301900

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references
  • Version 1.2: 2022-06-01
    Changes: Database references