1tjj

Human GM2 Activator Protein PAF complex

Method: X-RAY DIFFRACTION

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

Ganglioside GM2 activator

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ACETATE ION × 2 CHLORIDE ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 (2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate × 1 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ISOPROPYL ALCOHOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ACETATE ION × 2 CHLORIDE ION × 1 (2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate × 1 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ISOPROPYL ALCOHOL × 1 LAURIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ACETATE ION × 1 CHLORIDE ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 (2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate × 1 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ISOPROPYL ALCOHOL × 3 water × 1	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	ACETATE ION × 5 CHLORIDE ION × 3 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 (2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate × 3 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3 ISOPROPYL ALCOHOL × 5 LAURIC ACID × 1 water × 3	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	ACETATE ION × 4 CHLORIDE ION × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 (2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate × 2 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ISOPROPYL ALCOHOL × 2 LAURIC ACID × 1 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	ACETATE ION × 4 CHLORIDE ION × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 (2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate × 2 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ISOPROPYL ALCOHOL × 2 LAURIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAP3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–164； UniProt 31–192 Author chain B； PDBConstruct 3–164； UniProt 31–192 Author chain C； PDBConstruct 3–164； UniProt 31–192

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	1tjj
Deposition date deposition_date	2004-06-04
Structure title title	Human GM2 Activator Protein PAF complex
Keywords keywords	platelet activating factor, lipid binding pocket, beta-cup topology, protein dynamics, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

1tjj__assembly_1__model_1

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

Download this curve (.dat)

1tjj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tjj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.40 Å
Rg (electron density)	16.05 Å
Total Rg	17.05 Å
Atom count	1338
Residues	164
Excluded volume	24504 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tjj__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1tjj__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1tjj__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1tjj__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1tjj__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1tjj__assembly_6__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	Ganglioside GM2 activator
Molecular weight formula_weight	17827.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4578

HMSSFSWDNCDEGKDPAVIRSLTLEPDPIVVPGNVTLSVVGSTSVPLSSPLKVDLVLEKEVAGLWIKIPCTDYIGSCTFEHFCDVLDMLIPTGEPCPEPLRTYGLPCHCPFKEGTYSLPKSEFVVPDLELPSWLTTGNYRIESVLSSSGKRLGCIKIAASLKGI

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	(2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate
Molecular weight formula_weight	523.7 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	510.7 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 8 Entity 8 non-polymer

Description description	LAURIC ACID
Molecular weight formula_weight	200.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	568

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1tjja1
Class class	b — All beta proteins
Fold Fold fold	b.95 — Ganglioside M2 (gm2) activator
Superfamily Superfamily superfamily	b.95.1 — Ganglioside M2 (gm2) activator
Family Family family	b.95.1.1 — Ganglioside M2 (gm2) activator

Domain ID domain_id	d1tjja2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1tjjb1
Class class	b — All beta proteins
Fold Fold fold	b.95 — Ganglioside M2 (gm2) activator
Superfamily Superfamily superfamily	b.95.1 — Ganglioside M2 (gm2) activator
Family Family family	b.95.1.1 — Ganglioside M2 (gm2) activator

Domain ID domain_id	d1tjjb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1tjjc1
Class class	b — All beta proteins
Fold Fold fold	b.95 — Ganglioside M2 (gm2) activator
Superfamily Superfamily superfamily	b.95.1 — Ganglioside M2 (gm2) activator
Family Family family	b.95.1.1 — Ganglioside M2 (gm2) activator

Domain ID domain_id	d1tjjc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	1tjjA00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	220 — Ganglioside M2 Activator Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Ganglioside GM2 activator

Domain ID domain_id	1tjjB00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	220 — Ganglioside M2 Activator Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Ganglioside GM2 activator

Domain ID domain_id	1tjjC00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	220 — Ganglioside M2 Activator Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Ganglioside GM2 activator

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Unit-cell length a length_a	63.470 Å
Unit-cell length b length_b	86.510 Å
Unit-cell length c length_c	120.470 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	19.790 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	0.2340

Human GM2 Activator Protein PAF complex

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

Ganglioside GM2 activator

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

1tjj__assembly_1__model_1

1tjj__assembly_1__model_1 | I(q)

1tjj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Human GM2 Activator Protein PAF complex

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

Ganglioside GM2 activator

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

1tjj__assembly_1__model_1

1tjj__assembly_1__model_1 | I(q)

1tjj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)