7kmt

Structure of the yeast TRAPPIII-Ypt1(Rab1) complex

Method: ELECTRON MICROSCOPY

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

Trafficking protein particle complex subunit 23

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Trafficking protein particle complex subunit 31 × 1 （Q03337） Trafficking protein particle complex subunit BET5 × 1 （Q03630） Trafficking protein particle complex subunit BET3 × 2 （P36149） Trafficking protein particle complex subunit 33 × 1 （Q99394） Trafficking protein particle complex subunit 20 × 1 （P38334） GTP-binding protein YPT1 × 1 （P01123） Trafficking protein particle complex III-specific subunit 85 × 1 （P46944） PALMITIC ACID × 2	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 H； PDBConstruct 1–219； UniProt 1–219

Trafficking protein particle complex subunit 31

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 9	Trafficking protein particle complex subunit 23 × 1 （Q03784） Trafficking protein particle complex subunit BET5 × 1 （Q03630） Trafficking protein particle complex subunit BET3 × 2 （P36149） Trafficking protein particle complex subunit 33 × 1 （Q99394） Trafficking protein particle complex subunit 20 × 1 （P38334） GTP-binding protein YPT1 × 1 （P01123） Trafficking protein particle complex III-specific subunit 85 × 1 （P46944） PALMITIC ACID × 2	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 J； PDBConstruct 1–283； UniProt 1–283

Trafficking protein particle complex subunit BET5

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 9	Trafficking protein particle complex subunit 23 × 1 （Q03784） Trafficking protein particle complex subunit 31 × 1 （Q03337） Trafficking protein particle complex subunit BET3 × 2 （P36149） Trafficking protein particle complex subunit 33 × 1 （Q99394） Trafficking protein particle complex subunit 20 × 1 （P38334） GTP-binding protein YPT1 × 1 （P01123） Trafficking protein particle complex III-specific subunit 85 × 1 （P46944） PALMITIC ACID × 2	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 G； PDBConstruct 1–159； UniProt 1–159

Trafficking protein particle complex subunit BET3

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 9	Trafficking protein particle complex subunit 23 × 1 （Q03784） Trafficking protein particle complex subunit 31 × 1 （Q03337） Trafficking protein particle complex subunit BET5 × 1 （Q03630） Trafficking protein particle complex subunit 33 × 1 （Q99394） Trafficking protein particle complex subunit 20 × 1 （P38334） GTP-binding protein YPT1 × 1 （P01123） Trafficking protein particle complex III-specific subunit 85 × 1 （P46944） PALMITIC ACID × 2	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 F； PDBConstruct 1–193； UniProt 1–193 Author chain I； PDBConstruct 1–193； UniProt 1–193

Trafficking protein particle complex subunit 33

Saccharomyces cerevisiae

UniProt Q99394

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Trafficking protein particle complex subunit 23 × 1 （Q03784） Trafficking protein particle complex subunit 31 × 1 （Q03337） Trafficking protein particle complex subunit BET5 × 1 （Q03630） Trafficking protein particle complex subunit BET3 × 2 （P36149） Trafficking protein particle complex subunit 20 × 1 （P38334） GTP-binding protein YPT1 × 1 （P01123） Trafficking protein particle complex III-specific subunit 85 × 1 （P46944） PALMITIC ACID × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRS33_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–268； UniProt 1–268

Trafficking protein particle complex subunit 20

Saccharomyces cerevisiae

UniProt P38334

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Trafficking protein particle complex subunit 23 × 1 （Q03784） Trafficking protein particle complex subunit 31 × 1 （Q03337） Trafficking protein particle complex subunit BET5 × 1 （Q03630） Trafficking protein particle complex subunit BET3 × 2 （P36149） Trafficking protein particle complex subunit 33 × 1 （Q99394） GTP-binding protein YPT1 × 1 （P01123） Trafficking protein particle complex III-specific subunit 85 × 1 （P46944） PALMITIC ACID × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRS20_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain K； PDBConstruct 1–175； UniProt 1–175

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 9	Trafficking protein particle complex subunit 23 × 1 （Q03784） Trafficking protein particle complex subunit 31 × 1 （Q03337） Trafficking protein particle complex subunit BET5 × 1 （Q03630） Trafficking protein particle complex subunit BET3 × 2 （P36149） Trafficking protein particle complex subunit 33 × 1 （Q99394） Trafficking protein particle complex subunit 20 × 1 （P38334） Trafficking protein particle complex III-specific subunit 85 × 1 （P46944） PALMITIC ACID × 2	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	7
Chains and sequence ranges	Author chain A； PDBConstruct 1–206； UniProt 1–206

Trafficking protein particle complex III-specific subunit 85

Saccharomyces cerevisiae

UniProt P46944

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Trafficking protein particle complex subunit 23 × 1 （Q03784） Trafficking protein particle complex subunit 31 × 1 （Q03337） Trafficking protein particle complex subunit BET5 × 1 （Q03630） Trafficking protein particle complex subunit BET3 × 2 （P36149） Trafficking protein particle complex subunit 33 × 1 （Q99394） Trafficking protein particle complex subunit 20 × 1 （P38334） GTP-binding protein YPT1 × 1 （P01123） PALMITIC ACID × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRS85_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain B； PDBConstruct 20–717； UniProt 1–698

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	7kmt
Deposition date deposition_date	2020-11-03
Structure title title	Structure of the yeast TRAPPIII-Ypt1(Rab1) complex
Keywords keywords	GTPase, GEF, ER, Golgi, Autophagy, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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.

7kmt__assembly_1__model_1

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

Download this curve (.dat)

7kmt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7kmt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	60.09 Å
Rg (electron density)	62.26 Å
Total Rg	61.85 Å
Atom count	14945
Residues	1838
Excluded volume	269140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7kmt__assembly_1__model_1`	nonameric （9）	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	Trafficking protein particle complex subunit 23
Molecular weight formula_weight	24889.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	14945

MAIETILVINKSGGLIYQRNFTNDEQKLNSNEYLILASTLHGVFAIASQLTPKALQLTQQTNIENTIPYIPYVGMSSNRSDTRNGGGNNNKHTNNEKLGSFKGDDFFKEPFTNWNKSGLRQLCTDQFTMFIYQTLTGLKFVAISSSVMPQRQPTIATTDKPDRPKSTSNLAIQIADNFLRKVYCLYSDYVMKDPSYSMEMPIRSNLFDEKVKKMVENLQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Trafficking protein particle complex subunit 31
Molecular weight formula_weight	31755.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MSQRIIQPSASDQQFPGKSDGYEYTVGPKQAITSEASTTYIPSRIYSESLLFKRQEASLSAMAFLFQEMISQLHRTCKTAGDFETKLSDYGHNIGIRLLELLNFRASVSPSSLPRASAFLSQNESSSKLSNASNSPGMLANSSTATSASANERLQEKQTESLSNYITKMRRRDLKILDILQFIHGTLWSYLFNHVSDDLVKSSERDNEYMIVDNFPTLTQFIPGENVSCEYFVCGIIKGFLFNAGFPCGVTAHRMPQGGHSQRTVYLIQFDRQVLDREGLRFG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Trafficking protein particle complex subunit BET5
Molecular weight formula_weight	18453.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MGIYSFWIFDRHCNCIFDREWTLASNSASGTINSKQNEEDAKLLYGMIFSLRSITQKLSKGSVKNDIRSISTGKYRVHTYCTASGLWFVLLSDFKQQSYTQVLQYIYSHIYVKYVSNNLLSPYDFAENENEMRGQGTRKITNRNFISVLESFLAPMVNQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Trafficking protein particle complex subunit BET3
Molecular weight formula_weight	22152.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MVSTTQSRSLKAMGEEIWKNKTEKINTELFTLTYGSIVAQLCQDYERDFNKVNDHLYSMGYNIGCRLIEDFLARTALPRCENLVKTSEVLSKCAFKIFLNITPNITNWSHNKDTFSLILDENPLADFVELPMDAMKSLWYSNILCGVLKGSLEMVQLDCDVWFVSDILRGDSQTEIKVKLNRILKDEIPIGED

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Trafficking protein particle complex subunit 33
Molecular weight formula_weight	30786.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MSSTHSNNVGHPQSSPQGPLTEQQRAQQQYQIFENSLPKVSQSVYQMLLNEMVPLAMGIERQISGDVISSDSNVTSENGNINNMIKRLKIEEHHTVDIIRSHNLIHELYKADEEEKEKVLARLRNIGFQIGLKLSELLIFSNNPNLKFKEMDLLLIMKFICRDVWKQIFGKQIDNLKTNHRGTFYLLDYDYRPIQSFSLEEDAKNEELKMIEPFLEIPVGIIRGVLSSLGYSSEEVICLASFIDRPTDRPKTAFPKGVSFHVQVTMPQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Trafficking protein particle complex subunit 20
Molecular weight formula_weight	19721.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MPQYFAIIGKKDNPVYEIEFTNAENPQGFPQDLKELNPFILHASLDIVEDLQWQINPTSQLNGNGGNGSNGGGGFLRSRAVNNTDNCYLGKVDHFYGLAITAYISYSGMKFVMIHGNSANSSVVIDDNNMRSFYQEVHELYVKTLMNPFYKITDPIRSPAFDSRVRTLARKHLSK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	GTP-binding protein YPT1
Molecular weight formula_weight	23240.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MNSEYDYLFKLLLIGNSGVGKSCLLLRFSDDTYTNDYISTIGVDFKIKTVELDGKTVKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYATSTVLKLLVGNKCDLKDKRVVEYDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQIKESMSQQNLNETTQKKEDKGNVNLKGQSLTNTGGGCC

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Trafficking protein particle complex III-specific subunit 85
Molecular weight formula_weight	82850.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSQENLYFQGMVFSYEHYMNLLFHLDNSKETVPPEIAKRIISNAIAPVITVTSTPLFDKHIQETYKVDSLYMLLRFFGGCVSDRDQANEAKVGQHEHEVCDASDSTDSIPKNKNLEVPNLSKKGSRSRSNSLFQRDSTQSQYIRFTRPLGDLIETRDANDMLFNYHSLEVFLDNYLKLVAANTDEMVPHNLLKKSIYHSFFSLAISSTNNLSPYETFNHPILSLIALDISNGEVYEDARDLLVNFKNLNHNTENFPIFMNTNEMLPVFLLCYNDDSQEEFEKCQALAKKLKKQLFVESILLALWKDSFIYDENSVIQLHQPVMSSLEEILFFLQAPTQTTLSLALINSIYDMLDYLVYDLMIPFMKRKVSFWEETILQPRKSLFNGAKFFKKFMNKNPVNGNHQHNSLTRDSQGNEYFASSSSEFLMRKLADWSMMLSDFKTAYSTYESLMDDLDAFPKYLASCIEWCAVSLLMGAQSIVTVKMIKNDINPLIERALATYENCSRIQRGKGKESNSLDVTEPVRSYETRCMILASELFLSLSNTWTSTPYAIQYLETILDECKLGPCSQIMVWERLSDCYNLRVDPRIKHRVGAMKKDAKDTEDLRGEHKYSTDHFTDEDILSEGLTRRRKAAFFRLIAAKKWAEQKQWRQVSWCLKDIESTYSEIKFLHGNGLILSKLKNQLNLKDVDSAPRPSEKNLTRTSVSFIG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 9 Entity 9 non-polymer

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

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7kmtA01
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	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	3.70 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	69315

Structure of the yeast TRAPPIII-Ypt1(Rab1) complex

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

Trafficking protein particle complex subunit 23

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 31

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 BET5

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 BET3

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 33

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 20

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

Trafficking protein particle complex III-specific subunit 85

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

7kmt__assembly_1__model_1

7kmt__assembly_1__model_1 | I(q)

7kmt__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