2j3w

The crystal structure of the bet3-trs31-sedlin complex.

Method: X-RAY DIFFRACTION

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

TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2

MUS MUSCULUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	ZGC 92866 × 1 （Q6DGL5） TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3 × 1 （O55013） PALMITIC ACID × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	ZGC 92866 × 1 （Q6DGL5） TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3 × 1 （O55013） PALMITIC ACID × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TPPC2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–142； UniProt 1–140 Author chain C； PDBConstruct 3–142； UniProt 1–140

ZGC 92866

BRACHYDANIO RERIO

UniProt Q6DGL5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2 × 1 （Q9CQP2） TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3 × 1 （O55013） PALMITIC ACID × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2 × 1 （Q9CQP2） TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3 × 1 （O55013） PALMITIC ACID × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6DGL5_DANRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–188； UniProt 1–188 Author chain F； PDBConstruct 1–188； UniProt 1–188

TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3

MUS MUSCULUS

UniProt O55013

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2 × 1 （Q9CQP2） ZGC 92866 × 1 （Q6DGL5） PALMITIC ACID × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2 × 1 （Q9CQP2） ZGC 92866 × 1 （Q6DGL5） PALMITIC ACID × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TPPC3_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 3–182； UniProt 1–180 Author chain E； PDBConstruct 3–182； UniProt 1–180

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	2j3w
Deposition date deposition_date	2006-08-23
Structure title title	The crystal structure of the bet3-trs31-sedlin complex.
Keywords keywords	;MULTISUBUNIT TETHERING FACTOR, TRAPP, PALMITATE, TRANSPORT, LIPOPROTEIN, ER-GOLGI TRANSPORT, ENDOPLASMIC RETICULUM, TRANSCRIPTION, GOLGI APPARATUS, VESICLE TRANSPORT ;; TRANSPORT
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.

2j3w__assembly_1__model_1

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

Download this curve (.dat)

2j3w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2j3w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.13 Å
Rg (electron density)	25.21 Å
Total Rg	25.94 Å
Atom count	3664
Residues	460
Excluded volume	65772 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2j3w__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2j3w__assembly_2__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2
Molecular weight formula_weight	16705.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7597

LEMSGSFYFVIVGHHDNPVFEMEFLPPGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEWFVSAFVTAGHMRFIMLHDVRQEDGIKNFFTDVYDLYIKFAMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	HOUSE MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	ZGC 92866
Molecular weight formula_weight	21059.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

MEVRFTRGKSAILERSLTRPKTEVSVSAFALLFSEMVQYCQSRVYSVSELQARLADMGQGVGASLLDVLVMREKNGKRETKVLNILLFIKVNVWKALFGKEADKLEQANDDDKTYYIIEKEPLINAYISVPKENSTLNCAAFTGGIVEAILTHSGFPAKVTVHWHKGTTLMIKFDESVIARDKALDGR

Source Source

Source organism organism	BRACHYDANIO RERIO
Common name common_name	ZEBRAFISH
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
Molecular weight formula_weight	20452.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

GAMSRQANRGTESKKMSSELFTLTYGALVTQLCKDYENDEDVNKQLDRMGYNIGVRLIEDFLARSNVGRCHDFRETADVIAKVAFKMYLGITPSITNWSPAGDEFSLILENNPLVDFVELPDNHSALIYSNLLCGVLRGALEMVQMAVEAKFVQDTLKGDGVTEIRMRFIRRIEDNLPAGEE

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	HOUSE MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 4 Entity 4 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	215

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2j3wa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.4 — SNARE-like
Family Family family	d.110.4.3 — Sedlin (SEDL)

Domain ID domain_id	d2j3wb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.278 — Ligand-binding domain in the NO signalling and Golgi transport
Superfamily Superfamily superfamily	d.278.1 — Ligand-binding domain in the NO signalling and Golgi transport
Family Family family	d.278.1.2 — TRAPP components

Domain ID domain_id	d2j3wc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.4 — SNARE-like
Family Family family	d.110.4.3 — Sedlin (SEDL)

Domain ID domain_id	d2j3wd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.278 — Ligand-binding domain in the NO signalling and Golgi transport
Superfamily Superfamily superfamily	d.278.1 — Ligand-binding domain in the NO signalling and Golgi transport
Family Family family	d.278.1.2 — TRAPP components

Domain ID domain_id	d2j3we_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.278 — Ligand-binding domain in the NO signalling and Golgi transport
Superfamily Superfamily superfamily	d.278.1 — Ligand-binding domain in the NO signalling and Golgi transport
Family Family family	d.278.1.2 — TRAPP components

Domain ID domain_id	d2j3wf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.278 — Ligand-binding domain in the NO signalling and Golgi transport
Superfamily Superfamily superfamily	d.278.1 — Ligand-binding domain in the NO signalling and Golgi transport
Family Family family	d.278.1.2 — TRAPP components

CATH v4.4 (6 domains)

Domain ID domain_id	2j3wA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2j3wB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	20 — Trafficking protein particle complex subunit 3

Domain ID domain_id	2j3wC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2j3wD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	20 — Trafficking protein particle complex subunit 3

Domain ID domain_id	2j3wE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	20 — Trafficking protein particle complex subunit 3

Domain ID domain_id	2j3wF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	20 — Trafficking protein particle complex subunit 3

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Unit-cell length a length_a	232.211 Å
Unit-cell length b length_b	63.063 Å
Unit-cell length c length_c	72.018 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2296
R_work r_work	0.2296
R_free r_free	0.2765

The crystal structure of the bet3-trs31-sedlin complex.

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

TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2

State in the Current Structure

Other States of the Same Protein in the Database

ZGC 92866

State in the Current Structure

Other States of the Same Protein in the Database

TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3

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

2j3w__assembly_1__model_1

2j3w__assembly_1__model_1 | I(q)

2j3w__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

The crystal structure of the bet3-trs31-sedlin complex.

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

TRAFFICKING PROTEIN PARTICLE COMPLEX PROTEIN 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ZGC 92866

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3

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

2j3w__assembly_1__model_1

2j3w__assembly_1__model_1 | I(q)

2j3w__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)