3cue

Crystal structure of a TRAPP subassembly activating the Rab Ypt1p

Method: X-RAY DIFFRACTION

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

Transport protein particle 23 kDa subunit

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRS23_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–219； UniProt 1–219 Author chain G； PDBConstruct 1–219； UniProt 1–219 Author chain M； PDBConstruct 1–219； UniProt 1–219 Author chain S； PDBConstruct 1–219； UniProt 1–219

Transport protein particle 31 kDa subunit

Saccharomyces cerevisiae

UniProt Q03337

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRS31_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–283； UniProt 1–283 Author chain H； PDBConstruct 1–283； UniProt 1–283 Author chain N； PDBConstruct 1–283； UniProt 1–283 Author chain T； PDBConstruct 1–283； UniProt 1–283

Transport protein particle 18 kDa subunit

Saccharomyces cerevisiae

UniProt Q03630

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 22 kDa subunit × 2 （P36149） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BET5_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–159； UniProt 1–159 Author chain I； PDBConstruct 1–159； UniProt 1–159 Author chain O； PDBConstruct 1–159； UniProt 1–159 Author chain U； PDBConstruct 1–159； UniProt 1–159

Transport protein particle 22 kDa subunit

Saccharomyces cerevisiae

UniProt P36149

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BET3_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–193； UniProt 1–193 Author chain E； PDBConstruct 1–193； UniProt 1–193 Author chain J； PDBConstruct 1–193； UniProt 1–193 Author chain K； PDBConstruct 1–193； UniProt 1–193 Author chain P； PDBConstruct 1–193； UniProt 1–193 Author chain Q； PDBConstruct 1–193； UniProt 1–193 Author chain V； PDBConstruct 1–193； UniProt 1–193 Author chain W； PDBConstruct 1–193； UniProt 1–193

GTP-binding protein YPT1

Saccharomyces cerevisiae

UniProt P01123

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） PALMITIC ACID × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） PALMITIC ACID × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） PALMITIC ACID × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	Transport protein particle 23 kDa subunit × 1 （Q03784） Transport protein particle 31 kDa subunit × 1 （Q03337） Transport protein particle 18 kDa subunit × 1 （Q03630） Transport protein particle 22 kDa subunit × 2 （P36149） PALMITIC ACID × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YPT1_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–206； UniProt 1–206 Author chain L； PDBConstruct 1–206； UniProt 1–206 Author chain R； PDBConstruct 1–206； UniProt 1–206 Author chain X； PDBConstruct 1–206； UniProt 1–206

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	3cue
Deposition date deposition_date	2008-04-16
Structure title title	Crystal structure of a TRAPP subassembly activating the Rab Ypt1p
Keywords keywords	;membrane traffic, GEF, tethering complex, Rab activation, guanine nucleotide exchange factor, Endoplasmic reticulum, ER-Golgi transport, Golgi apparatus, Transport, Lipoprotein, Palmitate, GTP-binding, Nucleotide-binding, Phosphoprotein, Prenylation, Protein transport ;; PROTEIN 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.

3cue__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3cue__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cue__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	36.98 Å
Rg (electron density)	36.89 Å
Total Rg	37.14 Å
Atom count	8194
Residues	1009
Excluded volume	147060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cue__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cue__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3cue__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3cue__assembly_4__model_1`	hexameric （6）	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 (6)

Entity 1 Entity 1 polymer

Description description	Transport protein particle 23 kDa subunit
Molecular weight formula_weight	24889.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G,M,S
Atom count atom_count	32776

MAIETILVINKSGGLIYQRNFTNDEQKLNSNEYLILASTLHGVFAIASQLTPKALQLTQQTNIENTIPYIPYVGMSSNRSDTRNGGGNNNKHTNNEKLGSFKGDDFFKEPFTNWNKSGLRQLCTDQFTMFIYQTLTGLKFVAISSSVMPQRQPTIATTDKPDRPKSTSNLAIQIADNFLRKVYCLYSDYVMKDPSYSMEMPIRSNLFDEKVKKMVENLQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Transport protein particle 31 kDa subunit
Molecular weight formula_weight	31755.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,H,N,T

MSQRIIQPSASDQQFPGKSDGYEYTVGPKQAITSEASTTYIPSRIYSESLLFKRQEASLSAMAFLFQEMISQLHRTCKTAGDFETKLSDYGHNIGIRLLELLNFRASVSPSSLPRASAFLSQNESSSKLSNASNSPGMLANSSTATSASANERLQEKQTESLSNYITKMRRRDLKILDILQFIHGTLWSYLFNHVSDDLVKSSERDNEYMIVDNFPTLTQFIPGENVSCEYFVCGIIKGFLFNAGFPCGVTAHRMPQGGHSQRTVYLIQFDRQVLDREGLRFG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Transport protein particle 18 kDa subunit
Molecular weight formula_weight	18453.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,I,O,U

MGIYSFWIFDRHCNCIFDREWTLASNSASGTINSKQNEEDAKLLYGMIFSLRSITQKLSKGSVKNDIRSISTGKYRVHTYCTASGLWFVLLSDFKQQSYTQVLQYIYSHIYVKYVSNNLLSPYDFAENENEMRGQGTRKITNRNFISVLESFLAPMVNQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Transport protein particle 22 kDa subunit
Molecular weight formula_weight	22152.4 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,J,K,P,Q,V,W

MVSTTQSRSLKAMGEEIWKNKTEKINTELFTLTYGSIVAQLCQDYERDFNKVNDHLYSMGYNIGCRLIEDFLARTALPRCENLVKTSEVLSKCAFKIFLNITPNITNWSHNKDTFSLILDENPLADFVELPMDAMKSLWYSNILCGVLKGSLEMVQLDCDVWFVSDILRGDSQTEIKVKLNRILKDEIPIGED

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	GTP-binding protein YPT1
Molecular weight formula_weight	23240.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,L,R,X

MNSEYDYLFKLLLIGNSGVGKSCLLLRFSDDTYTNDYISTIGVDFKIKTVELDGKTVKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYATSTVLKLLVGNKCDLKDKRVVEYDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQIKESMSQQNLNETTQKKEDKGNVNLKGQSLTNTGGGCC

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3cuef1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d3cuel1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d3cuer1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d3cuex1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (24 domains)

Domain ID domain_id	3cueA01
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	3cueB00
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	3cueC00
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	3cueD00
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	3cueE00
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	3cueF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3cueG01
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	3cueH00
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	3cueI00
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	3cueJ00
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	3cueK00
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	3cueL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3cueM01
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	3cueN00
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	3cueO00
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	3cueP00
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	3cueQ00
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	3cueR01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3cueS01
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	3cueT00
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	3cueU00
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	3cueV00
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	3cueW00
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	3cueX01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	115.120 Å
Unit-cell length b length_b	115.400 Å
Unit-cell length c length_c	290.070 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.700 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2650
R_work r_work	0.2650
R_free r_free	0.2990

Crystal structure of a TRAPP subassembly activating the Rab Ypt1p

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

Transport protein particle 23 kDa subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transport protein particle 31 kDa subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transport protein particle 18 kDa subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transport protein particle 22 kDa subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GTP-binding protein YPT1

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

3cue__assembly_3__model_1

3cue__assembly_3__model_1 | I(q)

3cue__assembly_3__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 (6)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (4 domains)

CATH v4.4 (24 domains)

7. Citations (1)