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9ub7

Structure of glycosylphosphatidylinositol transamidase,state 1

Method: ELECTRON MICROSCOPY D_max: 158.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ub7
deposition_date	2025-04-02
title	Structure of glycosylphosphatidylinositol transamidase,state 1
keywords	GPI transamidase, GPI biosynthesis, Membrane protein; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	45.91 Å
rg_electron	45.79 Å
i0	1786380000.00
molecular_weight	241080.0 kDa
excluded_volume	237790 Å³
envelope_volume	467550 Å³
shell_volume	83816 Å³
envelope_diameter	175.0 Å
shell_rg	51.18 Å
envelope_rg	45.49 Å
shape_rg	45.80 Å
total_rg	45.96 Å
total_atoms	18334
n_residues	2272
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	158.2 Å
rg_real	45.93 Å
rg_real_error	1.62 Å
i0_real	1.7860e+09
i0_real_error	3.5700e+07
rg_reciprocal	45.91 Å
i0_reciprocal	1786000000.0000
total_estimate	0.8679
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	51.2 Å
skewness	0.393
kurtosis	-0.247
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	177700000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.881

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4. Crystallography & Experiment

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5. Entities & Polymer Info (14)

Entity 1 polymer

description	GPI transamidase component GAA1
formula_weight	69279.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	18334

MALLEKLHRRIVDMGLVPRIIALLPVISMLCALFGFISIAILPMDGQYRRTYISENALMPSQAYSYFRESEWNILRGYRSQIKEMVNMTSMERNNLMGSWLQEFGTKTAIYENEQYGETLYGVMHAPRGDGTEAMVLAVPWFNSDDEFNIGGAALGVSLARFFSRWPVWSKNIIVVFSENPRAALRSWVEAYHTSLDLTGGSIEAAVVLDYSSTEDFFEYVEISYDGLNGELPNLDLVNIAISITEHEGMKVSLHGLPSDQLTNNNFWSRLKILCLGIRDWALSGVKKPHGNEAFSGWRIQSVTLKAHGNSGHDITTFGRIPEAMFRSINNLLEKFHQSFFFYLLLAPRQFVSISSYLPSAVALSIAFAISSLNAFINNAYANISLFSEYNLVALLVWFVSLVISFVVSQAFLLIPSSGLLMTISMASCFLPLILSRKIHISEPLSYRLKNVAFLYFSLVSTSLLMINFAMALLIGTLAFPMTFVKTIVESSSEHEVTTQSSNPIKTEPKDEIELVENHMDTTPATPQQQKQKLKNLVLLILTNPFISITLFGLFFDDEFHGFDIINKLVSAWLDLKCWSWFVLCIGWLPCWLLILASSFESKSVVVRSKEKQS

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 2 polymer

description	GPI transamidase component GAB1
formula_weight	44768.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MDSTALKVALGCIAIRLAVNSLFPSLQQQLDQSVEFSTPVTSFRSLQEGIYLLRNNIQVYNHGVVHHPPILIFFLSLFNSDRLISLIYALIDGLIAYQLTEVTKAFKNLKLKVWLPGLLYAVNPLTLLSCISRSSIIFTNFAISSSLYCILAEGNVLLSSVMISISGYLSVYPILLLIPLLGMLKSWRQRILSAIVSILSLLILLLFSYSILGSQSWSFLTQVYGSIITFEKVFPNLGLWWYFFIEMFDTFIPFFKAVFNIFIAVFITPFTLRYHKQPFYAFILCIGWIVLTKPYPSLGDAGFFFSFLPFFTPLFGYLRYPIISALLFLHAIVLAPIFYHLWVVLGSGNSNFFYAISLVYALAIASILVDLNWAMLRIEYDNGIPNFKLKVTQI

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 3 polymer

description	GPI-anchor transamidase
formula_weight	47452.2 kDa
ec_number	3.-.-.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MRIAMHLPLLLLYIFLLPLSGANNTDAAHEVIATNTNNWAVLVSTSRFWFNYRHMANVLSMYRTVKRLGIPDSQIILMLSDDVACNSRNLFPGSVFNNKDHAIDLYGDSVEVDYRGYEVTVENFIRLLTDRWTEDHPKSKRLLTDENSNIFIYMTGHGGDDFLKFQDAEEIASEDIADAFQQMYEKKRYNEIFFMIDTCQANTMYSKFYSPNILAVGSSEMDESSYSHHSDVEIGVAVIDRFTYYCLDFLEQIDKNSTLTLQDLFDSFTFEKIHSHVGVRTDLFDRNPSEVLITDFFANVQNVIPDDSKPLSVSHYHHYKDHIDTAQYELNNNVLDLALETYRKNNQSSKIEKKIKDIKSTSVLDVDIDSNECFFTSFKQSATIILALIVTILWFMLRGNTAKATYDLYTN

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 4 polymer

description	GPI transamidase component GPI17
formula_weight	60862.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MSNANLRKWVGFCFVAIYLFLGVPLWYKLTTVYRASLPINYIESLQNNKFQDIHLVIPVYVKSDTYRFPDVHDAIQVQVNHLLNSQEQRVPWSLQVLPYNETIEQMESEGNQFHVVTLKLDEFIGYSSAYDTKETLVYYDDAAVLSNDLPFFVAQTLVEHTFQLEWTHLNKTCEGVSTNNDVAISYDPNIHLSVTLLSGDGNPVAWEIEPTLTDYFSPFRKFLSPLVNFTVDSSIVYHNDLNLHSLNGSCTSVTWFDLSHTIDLSELSSMAYYPEDSALNLAIVFPSASSSPDGLAFINGTRISDEITTLDWNSYLVPQWGVIIINKMPLKPNSVISEDYLEPMMYRFATDIFQLLGLTEGSQDLLSPYITIDSFKRLTILQNLDKATETLWSLVKLTQQFQGMSIPREVSDNVIEALDLRLQIIDLLNDPGKGGDIVWNNALHLSNELVKLCEKAFFNGEMVQQNFFPQEHMIAVYLPLLGPISAVMFFGFYNVMKEKNQKSKKNGTEREVAKEKLELKEAQKLHAIDGEDEL

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 5 polymer

description	GPI transamidase component GPI16
formula_weight	68836.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MILTLAYFMLGTLLLGVFAEDTVSQIGINDSLWYPYDEALVLKPLPNNDLLLSFAFQLQSEPFDPAVSSMSYDAYEHYTTFPRAIPPLLESTATRQFHLRFTRGFWDALSWGQLPHAGKEAGASGVELWSQVQAMDQEQAFHNWKKLSNSLSGLFCSSLNFIDESRTTFPRRSYASDIGAPLFNSTEKLYLMRASLPNEPICTENLTPFIKLLPTRGKSGLTSLLDGHKLFDSLWNSISLDIATICSEDEDALCHYEMDARIEMVTHVPSALARGERPIPKPLDGNTLRCDTDKPFDSYQCFPLPEPSQTHFKLSQLFARPINNGNLFANRPTRICAEVDRSTWTAFLSVDDTIFSTHDNCFDLSNDQNEGGSGYDFILESTDTTKVTPIVPVPIHVSRSLTGNGQDRGGMRIVFHNDNDTPVKLIYFESLPWFMRVYLSSLQITSTTSPQLQENDIILDKYYLQAADRKRPGHLEFTMLIPANTDIVMTYQFDKALLQFAEYPPDANHGFEIDAAVITVLSLESSSSLYEMRTSTLLLSLSTPDFSMPYNVIILTSTIMGLIFGMLYNLMVKRMVTVEEADKITLQSGLKYKLLKLKEKFLGKKKTKTD

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 6 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

Entity 7 branched

description	;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 ;
formula_weight	748.7 kDa
src_method	man
entity_count	1

Entity 8 non-polymer

description	CHOLESTEROL HEMISUCCINATE
formula_weight	486.7 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	(11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate
formula_weight	495.6 kDa
src_method	syn
entity_count	2

Entity 10 non-polymer

description	TETRADECANE
formula_weight	198.4 kDa
src_method	syn
entity_count	3

Entity 11 non-polymer

description	DODECANE
formula_weight	170.3 kDa
src_method	syn
entity_count	3

Entity 12 non-polymer

description	DECANE
formula_weight	142.3 kDa
src_method	syn
entity_count	1

Entity 13 non-polymer

description	;[(2~{R})-1-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-azanyl-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-heptanoyloxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-3-decoxy-propan-2-yl] nonanoate ;
formula_weight	888.0 kDa
src_method	syn
entity_count	1

Entity 14 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.61 Å
resolution_method	—
num_particles	55376

fit	/app/data/saxs_computation/ub/9ub7/9ub7.fit
pddf	/app/data/pr_computation/ub/9ub7/9ub7.pr.out
profile	/app/data/saxs_computation/ub/9ub7/9ub7.dat

Structure of glycosylphosphatidylinositol transamidase,state 1

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (14)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 branched

Entity 7 branched

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

Entity 14 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)