7WLD | pdb_00007wld

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

PDB DOI: https://doi.org/10.2210/pdb7WLD/pdb
EM Map EMD-32582: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2022-01-13 Released: 2022-04-27
Deposition Author(s): Xu, Y., Li, T., Luo, Y., Chao, Y., Jia, G., Zhou, Z., Su, Z., Qu, Q., Li, D.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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

PubMed: 35551457 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-30250-6
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 451.01 kDa
Atom Count: 19,732
Modeled Residue Count: 2,393
Deposited Residue Count: 3,892
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosylphosphatidylinositol anchor attachment 1 protein	A [auth G]	886	Homo sapiens	Mutation(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
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43292
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth G]	Go to GlyGen: O43292-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GPI-anchor transamidase	B [auth K]	647	Homo sapiens	Mutation(s): 0 Gene Names: PIGK EC: 3 (PDB Primary Data), 2.6.1 (UniProt) 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92643
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GPI transamidase component PIG-S	C [auth S]	816	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96S52
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth S]	Go to GlyGen: Q96S52-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
GPI transamidase component PIG-T	D [auth T]	831	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q969N2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D [auth T]	Go to GlyGen: Q969N2-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol glycan anchor biosynthesis class U protein	E [auth U]	712	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H490
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain Y [auth U] MOL2 format, chain Y [auth U] mmCIF format, chain Y [auth U]	Y [auth U]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain Y [auth U] Interactions & Density Focus chain Y [auth U]
AJP Query on AJP Download:Ideal Coordinates CCD File SDF format, chain I [auth G] MOL2 format, chain I [auth G] mmCIF format, chain I [auth G]	I [auth G]	Digitonin C₅₆ H₉₂ O₂₉ UVYVLBIGDKGWPX-KUAJCENISA-N		Interactions Focus chain I [auth G] Interactions & Density Focus chain I [auth G]
06O (Subject of Investigation/LOI) Query on 06O Download:Ideal Coordinates CCD File SDF format, chain GA [auth U] MOL2 format, chain GA [auth U] mmCIF format, chain GA [auth U]	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		Interactions Focus chain GA [auth U] Interactions & Density Focus chain GA [auth U]
P5S Query on P5S Download:Ideal Coordinates CCD File SDF format, chain Q [auth K] MOL2 format, chain Q [auth K] mmCIF format, chain Q [auth K]	Q [auth K]	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine C₄₂ H₈₂ N O₁₀ P TZCPCKNHXULUIY-RGULYWFUSA-N		Interactions Focus chain Q [auth K] Interactions & Density Focus chain Q [auth K]
BJR Query on BJR Download:Ideal Coordinates CCD File SDF format, chain J [auth G] SDF format, chain K [auth G] MOL2 format, chain J [auth G] MOL2 format, chain K [auth G] mmCIF format, chain J [auth G] mmCIF format, chain K [auth G]	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		Interactions Focus chain J [auth G] Focus chain K [auth G] Interactions & Density Focus chain J [auth G] Focus chain K [auth G]
PEE Query on PEE Download:Ideal Coordinates CCD File SDF format, chain L [auth G] MOL2 format, chain L [auth G] mmCIF format, chain L [auth G]	L [auth G]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain L [auth G] Interactions & Density Focus chain L [auth G]
DKB Query on DKB Download:Ideal Coordinates CCD File SDF format, chain CA [auth U] MOL2 format, chain CA [auth U] mmCIF format, chain CA [auth U]	CA [auth U]	[(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate C₃₉ H₇₈ N O₈ P RPJZYOHZALDGKI-DIPNUNPCSA-N		Interactions Focus chain CA [auth U] Interactions & Density Focus chain CA [auth U]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain DA [auth U] SDF format, chain EA [auth U] SDF format, chain FA [auth U] SDF format, chain G SDF format, chain H [auth G] SDF format, chain M [auth G] SDF format, chain N [auth G] SDF format, chain O [auth G] SDF format, chain Z [auth U] MOL2 format, chain DA [auth U] MOL2 format, chain EA [auth U] MOL2 format, chain FA [auth U] MOL2 format, chain G MOL2 format, chain H [auth G] MOL2 format, chain M [auth G] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G] MOL2 format, chain Z [auth U] mmCIF format, chain DA [auth U] mmCIF format, chain EA [auth U] mmCIF format, chain FA [auth U] mmCIF format, chain G mmCIF format, chain H [auth G] mmCIF format, chain M [auth G] mmCIF format, chain N [auth G] mmCIF format, chain O [auth G] mmCIF format, chain Z [auth U]	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		Interactions Focus chain DA [auth U] Focus chain EA [auth U] Focus chain FA [auth U] Focus chain G Focus chain H [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Focus chain Z [auth U] Interactions & Density Focus chain DA [auth U] Focus chain EA [auth U] Focus chain FA [auth U] Focus chain G Focus chain H [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Focus chain Z [auth U]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain AA [auth U] SDF format, chain BA [auth U] SDF format, chain S SDF format, chain T [auth S] SDF format, chain U [auth S] MOL2 format, chain AA [auth U] MOL2 format, chain BA [auth U] MOL2 format, chain S MOL2 format, chain T [auth S] MOL2 format, chain U [auth S] mmCIF format, chain AA [auth U] mmCIF format, chain BA [auth U] mmCIF format, chain S mmCIF format, chain T [auth S] mmCIF format, chain U [auth S]	AA [auth U], BA [auth U], S, T [auth S], U [auth S]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain AA [auth U] Focus chain BA [auth U] Focus chain S Focus chain T [auth S] Focus chain U [auth S] Interactions & Density Focus chain AA [auth U] Focus chain BA [auth U] Focus chain S Focus chain T [auth S] Focus chain U [auth S]
05E (Subject of Investigation/LOI) Query on 05E Download:Ideal Coordinates CCD File SDF format, chain V [auth T] MOL2 format, chain V [auth T] mmCIF format, chain V [auth T]	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		Interactions Focus chain V [auth T] Interactions & Density Focus chain V [auth T]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain R [auth S] SDF format, chain W [auth T] MOL2 format, chain R [auth S] MOL2 format, chain W [auth T] mmCIF format, chain R [auth S] mmCIF format, chain W [auth T]	R [auth S], W [auth T]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain R [auth S] Focus chain W [auth T] Interactions & Density Focus chain R [auth S] Focus chain W [auth T]
PA1 (Subject of Investigation/LOI) Query on PA1 Download:Ideal Coordinates CCD File SDF format, chain X [auth T] MOL2 format, chain X [auth T] mmCIF format, chain X [auth T]	X [auth T]	2-amino-2-deoxy-alpha-D-glucopyranose C₆ H₁₃ N O₅ MSWZFWKMSRAUBD-UKFBFLRUSA-N		Interactions Focus chain X [auth T] Interactions & Density Focus chain X [auth T]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth K] MOL2 format, chain P [auth K] mmCIF format, chain P [auth K]	P [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain P [auth K] Interactions & Density Focus chain P [auth K]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82151215
National Natural Science Foundation of China (NSFC)	China	31870726
National Natural Science Foundation of China (NSFC)	China	82041016
National Natural Science Foundation of China (NSFC)	China	32070049
Ministry of Science and Technology (MoST, China)	China	2021YFA1301900