8k9r

Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

GPI inositol-deacylase,MCherry protein

Psychromonas sp. B3M02

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Green fluorescent protein,Complement decay-accelerating factor × 1 （P08174） alpha-D-mannopyranose × 2 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate × 1 2-amino-2-deoxy-alpha-D-glucopyranose × 1 ;[(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] octadecanoate ; × 1 PALMITIC ACID × 1 CHOLESTEROL × 1 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A366VY15_9GAMM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1201–1435； UniProt 2–236

GPI inositol-deacylase,MCherry protein

Psychromonas sp. B3M02

UniProt G0S652

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Green fluorescent protein,Complement decay-accelerating factor × 1 （P08174） alpha-D-mannopyranose × 2 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate × 1 2-amino-2-deoxy-alpha-D-glucopyranose × 1 ;[(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] octadecanoate ; × 1 PALMITIC ACID × 1 CHOLESTEROL × 1 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0S652_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–1186； UniProt 2–1184

Green fluorescent protein,Complement decay-accelerating factor

Homo sapiens

UniProt P08174

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	GPI inositol-deacylase,MCherry protein × 1 （A0A366VY15,G0S652） alpha-D-mannopyranose × 2 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate × 1 2-amino-2-deoxy-alpha-D-glucopyranose × 1 ;[(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] octadecanoate ; × 1 PALMITIC ACID × 1 CHOLESTEROL × 1 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DAF_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 264–272； UniProt 345–353

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8k9r
Deposition date deposition_date	2023-08-01
Structure title title	Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum
Keywords keywords	;Bst1, Glycosylphosphatidylinositol, GPI anchoring, GPI-AP, GPI-AP remodelase, Integral membrane enzyme, Lipase, Lipid remodeling, Membrane enzyme, Membrane protein, Nanodisc, PGAP1, TGP, Thermostable green fluorescence protein, Transmembrane enzyme, Triad enzyme. ;; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8k9r__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8k9r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8k9r__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	33.63 Å
Rg (electron density)	33.10 Å
Total Rg	33.56 Å
Atom count	7684
Residues	962
Excluded volume	138700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8k9r__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	GPI inositol-deacylase,MCherry protein
Molecular weight formula_weight	161337.5 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	H443N,W148S,I166V,Q168Y,I202R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7684

MGSRSLSSASSDDDDAPPIRVPRVNQCATSRTKDSQSPAQSASKLDRRRSADRRPSFSANRRSGTGAGTGTGTGIANWRPFDSRDATVERAGSSTATTATTPPPSSSLGLMLAANGAVQEKEMVMMGKAQEHGFVGRRAPWRSPWAISVFAFVTSLLGIGLLLAVIHSSVTRQIDPKGCRMSYMRPSYAKLSDFDTEHTRLASKYSLYLYREQGIDHDVKVRGVPVLFIPGNAGSYKQVRPIAAEAANYFHDVLQHDEAALRAGVRSLDFFTVDFNEDITAFHGQTLLDQAEYLNEAIRYILSLYLDPRVSERDPDLPDPTSVIVLGHSMGGIVARTMLIMPNYQHNSINTIITMSAPHARPPVSFDGQIVQTYKDINNYWRHAYSQKWANDNPLWHVTLVSIAGGGLDTVVPSDYASIESLVPDTHGFTVFTSTIPNVWTSMDNQAILWCDQFRKVIIRALFDIVDVHRASQTKPRAQRMRVFKKWFLSGMETVAEKIAPTSDPTTLLIVDDKSDSITAEGERLVLRELGTQGSVRAHLMPIPPPGSPELKRFTLLTDTKLDKPGENGKLEVMFCSVIPSQPNPTGPAIPSQLDLSKGNAGTTRLACTNVAPDVITLPASTRFARFPFSVRKEAEIPPFSYLEYVLDDISEHQFVAVIEKATIPTPGFVIAEFSDHSNSHHTRHIGLRNLLTFGISLRLPSNRPMMSEVRIPSVKSSLLAYNLRISALECSGRKDLFAPLVRQYLAEPYESKYFVNARQAAVSLHGVAPYVPPPMSREPEAEGLAFQLWTDPTCNSSIQVDLTVDVMGSLGKLYMRYRTVFAAFPLFIVSLVLRKQFQVYDSTGSFITFAEGLDLSLRQSIPVMLIVLAALTLSTTKMAPSSSAGLWHWGGNTTFTNFHQNDLLIGTQDPFFLFLIPLIGIICVGVCTVVNYIALSLTRLISVVISFIGFLTVRFGWVNAEDRRRPSNPAIFPPSSPRRRMITTAVLLFLVSTMIPYQLAYLVACLVQLGTLVRAQRISSELRSPANSNFHNYVHSIFILMLWILPINLPTLVVWMHNLSVHWLTPFTSHHNVFSIMPFILLVETHTTGQMIPRTGGTGNGRCCVLLRHITSILLLSLALYAAVYGVSYAYTLHQFVNLFAFWLVMVHSTADDWSLTGLRQLILHNRNNANNKSETGSRKRGKEPGTLEVLFQGPKLEFVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGSEASSERMYPEDGALKGEVKYRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNRKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYKSAHHHHHHHHHH

Source Source

Source organism organism	Psychromonas sp. B3M02
NCBI taxonomy ID ncbi_taxonomy_id	2267226
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Green fluorescent protein,Complement decay-accelerating factor
Molecular weight formula_weight	29894.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GGSGGSASVIKPEMKIKLRMEGAVNGHKFVIEGEGIGKPYEGTQTLDLTVEEGAPLPFSYDILTPAFQYGNRAFTKYPEDIPDYFKQAFPEGYSWERSMTYEDQGICIATSDITMEGDCFFYEIRFDGTNFPPNGPVMQKKTLKWEPSTEKMYVEDGVLKGDVEMALLLEGGGHYRCDFKTTYKAKKDVRLPDAHEVDHRIEILSHDKDYNKVRLYEHAEARYSGGGSGGGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKGSPNKGSGTTS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate
Molecular weight formula_weight	303.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-amino-2-deoxy-alpha-D-glucopyranose
Molecular weight formula_weight	179.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	;[(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] octadecanoate ;
Molecular weight formula_weight	853.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate
Molecular weight formula_weight	303.2 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.68 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	179980

Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum

1. Protein Identity and Related Structures Protein Identity & Related Structures

GPI inositol-deacylase,MCherry protein

State in the Current Structure

Other States of the Same Protein in the Database

GPI inositol-deacylase,MCherry protein

State in the Current Structure

Other States of the Same Protein in the Database

Green fluorescent protein,Complement decay-accelerating factor

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8k9r__assembly_1__model_1

8k9r__assembly_1__model_1 | I(q)

8k9r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

7. Citations (1)

Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum

1. Protein Identity and Related Structures Protein Identity & Related Structures

GPI inositol-deacylase,MCherry protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GPI inositol-deacylase,MCherry protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Green fluorescent protein,Complement decay-accelerating factor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8k9r__assembly_1__model_1

8k9r__assembly_1__model_1 | I(q)

8k9r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

7. Citations (1)