7kai

Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62, conformation 1 (C1)

Method: ELECTRON MICROSCOPY

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

Protein transport protein SEC61

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein transport protein SSS1 × 1 （P35179） Protein transport protein SBH1 × 1 （P52870） Protein translocation protein SEC63 × 1 （P14906） Translocation protein SEC66 × 1 （P33754） Translocation protein SEC72 × 1 （P39742） Protein transport protein Sec62 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SC61A_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–480； UniProt 1–480

Protein transport protein SSS1

OrganismNot specified

UniProt P35179

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein transport protein SEC61 × 1 （P32915） Protein transport protein SBH1 × 1 （P52870） Protein translocation protein SEC63 × 1 （P14906） Translocation protein SEC66 × 1 （P33754） Translocation protein SEC72 × 1 （P39742） Protein transport protein Sec62 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SC61G_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–80； UniProt 1–80

Protein transport protein SBH1

OrganismNot specified

UniProt P52870

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein transport protein SEC61 × 1 （P32915） Protein transport protein SSS1 × 1 （P35179） Protein translocation protein SEC63 × 1 （P14906） Translocation protein SEC66 × 1 （P33754） Translocation protein SEC72 × 1 （P39742） Protein transport protein Sec62 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SC6B1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–82； UniProt 1–82

Protein translocation protein SEC63

Saccharomyces cerevisiae BY4741

UniProt P14906

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein transport protein SEC61 × 1 （P32915） Protein transport protein SSS1 × 1 （P35179） Protein transport protein SBH1 × 1 （P52870） Translocation protein SEC66 × 1 （P33754） Translocation protein SEC72 × 1 （P39742） Protein transport protein Sec62 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC63_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 16–677； UniProt 2–663

Translocation protein SEC66

OrganismNot specified

UniProt P33754

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein transport protein SEC61 × 1 （P32915） Protein transport protein SSS1 × 1 （P35179） Protein transport protein SBH1 × 1 （P52870） Protein translocation protein SEC63 × 1 （P14906） Translocation protein SEC72 × 1 （P39742） Protein transport protein Sec62 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC66_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–206； UniProt 1–206

Translocation protein SEC72

OrganismNot specified

UniProt P39742

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein transport protein SEC61 × 1 （P32915） Protein transport protein SSS1 × 1 （P35179） Protein transport protein SBH1 × 1 （P52870） Protein translocation protein SEC63 × 1 （P14906） Translocation protein SEC66 × 1 （P33754） Protein transport protein Sec62 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC72_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–193； UniProt 1–193

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	7kai
Deposition date deposition_date	2020-10-01
Structure title title	Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62, conformation 1 (C1)
Keywords keywords	Sec61, translocon, endoplasmic reticulum, protein translocation, Sec62, Sec63, channel, 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.

7kai__assembly_1__model_1

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

Download this curve (.dat)

7kai__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7kai__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.20 Å
Rg (electron density)	41.67 Å
Total Rg	42.07 Å
Atom count	10718
Residues	1399
Excluded volume	194550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7kai__assembly_1__model_1`	heptameric （7）	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 (7)

Entity 1 Entity 1 polymer

Description description	Protein transport protein SEC61
Molecular weight formula_weight	52978.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10718

MSSNRVLDLFKPFESFLPEVIAPERKVPYNQKLIWTGVSLLIFLILGQIPLYGIVSSETSDPLYWLRAMLASNRGTLLELGVSPIITSSMIFQFLQGTQLLQIRPESKQDRELFQIAQKVCAIILILGQALVVVMTGNYGAPSDLGLPICLLLIFQLMFASLIVMLLDELLSKGYGLGSGISLFTATNIAEQIFWRAFAPTTVNSGRGKEFEGAVIAFFHLLAVRKDKKRALVEAFYRTNLPNMFQVLMTVAIFLFVLYLQGFRYELPIRSTKVRGQIGIYPIKLFYTSNTPIMLQSALTSNIFLISQILFQKYPTNPLIRLIGVWGIRPGTQGPQMALSGLAYYIQPLMSLSEALLDPIKTIVYITFVLGSCAVFSKTWIEISGTSPRDIAKQFKDQGMVINGKRETSIYRELKKIIPTAAAFGGATIGALSVGSDLLGTLGSGASILMATTTIYGYYEAAAKEGGFTKNLVPGFSDLM

Entity 2 Entity 2 polymer

Description description	Protein transport protein SSS1
Molecular weight formula_weight	8958.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MARASEKGEEKKQSNNQVEKLVEAPVEFVREGTQFLAKCKKPDLKEYTKIVKAVGIGFIAVGIIGYAIKLIHIPIRYVIV

Entity 3 Entity 3 polymer

Description description	Protein transport protein SBH1
Molecular weight formula_weight	8723.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSSPTPPGGQRTLQKRKQGSSQKVAASAPKKNTNSNNSILKIYSDEATGLRVDPLVVLFLAVGFIFSVVALHVISKVAGKLF

Entity 4 Entity 4 polymer

Description description	Protein translocation protein SEC63
Molecular weight formula_weight	77933.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GGSGGSGGSGGSGGSPTNYEYDEASETWPSFILTGLLMVVGPMTLLQIYQIFFGANAEDGNSGKSKEFNEEVFKNLNEEYTSDEIKQFRRKFDKNSNKKSKIWSRRNIIIIVGWILVAILLQRINSNDAIKDAATKLFDPYEILGISTSASDRDIKSAYRKLSVKFHPDKLAKGLTPDEKSVMEETYVQITKAYESLTDELVRQNYLKYGHPDGPQSTSHGIALPRFLVDGSASPLLVVCYVALLGLILPYFVSRWWARTQSYTKKGIHNVTASNFVSNLVNYKPSEIVTTDLILHWLSFAHEFKQFFPDLQPTDFEKLLQDHINRRDSGKLNNAKFRIVAKCHSLLHGLLDIACGFRNLDIALGAINTFKCIVQAVPLTPNCQILQLPNVDKEHFITKTGDIHTLGKLFTLEDAKIGEVLGIKDQAKLNETLRVASHIPNLKIIKADFLVPGENQVTPSSTPYISLKVLVRSAKQPLIPTSLIPEENLTEPQDFESQRDPFAMMSKQPLVPYSFAPFFPTKRRGSWCCLVSSQKDGKILQTPIIIEKLSYKNLNDDKDFFDKRIKMDLTKHEKFDINDWEIGTIKIPLGQPAPETVGDFFFRVIVKSTDYFTTDLDITMNMKVRDSPAVEQVEVYSEEDDEYSTDDDETESDDESDASDYTDIDTDTEAEDDESPEAGGATTASGTGENLYFQ

Source Source

Source organism organism	Saccharomyces cerevisiae BY4741
NCBI taxonomy ID ncbi_taxonomy_id	1247190
Host organism host_organism	Saccharomyces cerevisiae BY4741

Entity 5 Entity 5 polymer

Description description	Translocation protein SEC66
Molecular weight formula_weight	24263.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MSEFNETKFSNNGTFFETEEPIVETKSISVYTPLIYVFILVVSLVMFASSYRKKQAKKISEQPSIFDENDAHDLYFQIKEMSENEKIHEKVLKAALLNRGAESVRRSLKLKELAPQINLLYKNGSIGEDYWKRFETEVKLIELEFKDTLQEAERLQPGWVQLFVMVCKEICFNQALSRRYQSILKRKEVCIKEWELKINNDGRLVN

Entity 6 Entity 6 polymer

Description description	Translocation protein SEC72
Molecular weight formula_weight	21631.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MVTLEYNANSKLITASDAVVALSTETNIDQINVLTTSLIGETNPNFTPQPNEALSKMIKGLFESGMKNLQQKKLNEALKNVSLAIEMAQRKRAPWEAFAIQLPELHFMLRSKIDLCLILGKHLEALQDLDFLLGTGLIQPDVFVRKADCLLKLRQWEEARATCERGLALAPEDMKLRALLIETARNLAEYNGE

Entity 7 Entity 7 polymer

Description description	Protein transport protein Sec62
Molecular weight formula_weight	4783.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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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	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	193263

Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62, conformation 1 (C1)

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

Protein transport protein SEC61

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein transport protein SSS1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein transport protein SBH1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein translocation protein SEC63

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Translocation protein SEC66

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Translocation protein SEC72

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

7kai__assembly_1__model_1

7kai__assembly_1__model_1 | I(q)

7kai__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

7. Citations (1)