6itc

Structure of a substrate engaged SecA-SecY protein translocation machine

Method: ELECTRON MICROSCOPY

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

Protein translocase subunit SecA

Bacillus subtilis (strain 168)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein translocase subunit SecY × 1 （A4IJK8） Protein translocase subunit SecE × 1 （A4IJH4） Nanobody × 1 Translocating peptide × 1 Green fluorescent protein × 1 （P42212） Nanobody × 1 MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–780； UniProt 1–780

Protein translocase subunit SecY

Geobacillus thermodenitrificans (strain NG80-2)

UniProt A4IJK8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecE × 1 （A4IJH4） Nanobody × 1 Translocating peptide × 1 Green fluorescent protein × 1 （P42212） Nanobody × 1 MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4IJK8_GEOTN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain Y； PDBConstruct 1–424； UniProt 1–430

Protein translocase subunit SecE

Geobacillus thermodenitrificans (strain NG80-2)

UniProt A4IJH4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecY × 1 （A4IJK8） Nanobody × 1 Translocating peptide × 1 Green fluorescent protein × 1 （P42212） Nanobody × 1 MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4IJH4_GEOTN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–60； UniProt 1–60

Green fluorescent protein

Aequorea victoria

UniProt P42212

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecY × 1 （A4IJK8） Protein translocase subunit SecE × 1 （A4IJH4） Nanobody × 1 Translocating peptide × 1 Nanobody × 1 MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GFP_AEQVI
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–236； UniProt 1–238

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	6itc
Deposition date deposition_date	2018-11-21
Structure title title	Structure of a substrate engaged SecA-SecY protein translocation machine
Keywords keywords	SecA, SecY, Translocation, Cryo-EM, 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.

6itc__assembly_1__model_1

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

Download this curve (.dat)

6itc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6itc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.29 Å
Rg (electron density)	44.00 Å
Total Rg	44.10 Å
Atom count	13841
Residues	1738
Excluded volume	247540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6itc__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 (11)

Entity 1 Entity 1 polymer

Description description	Protein translocase subunit SecA
Molecular weight formula_weight	88916.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	13844

MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDDLLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYDDVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDLINTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKAEI

Source Source

Source organism organism	Bacillus subtilis (strain 168)
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli #1/H766

Entity 2 Entity 2 polymer

Description description	Protein translocase subunit SecY
Molecular weight formula_weight	46768.3 kDa
Mutation mutation	G60C,Q202T,L210G,F211G,R213N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFCGGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVLGFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGISIIIFAGIVSGIPTILNQIYAQTFGGLNIVRLLLVALAVVAVIVGVIYIQQAFRKIPIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWIRRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYVTRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQLVKRHYRGFIK

Source Source

Source organism organism	Geobacillus thermodenitrificans (strain NG80-2)
NCBI taxonomy ID ncbi_taxonomy_id	420246
Host organism host_organism	Escherichia coli K-12

Entity 3 Entity 3 polymer

Description description	Protein translocase subunit SecE
Molecular weight formula_weight	8249.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MQRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVFEGGHHHHHHHH

Source Source

Source organism organism	Geobacillus thermodenitrificans (strain NG80-2)
NCBI taxonomy ID ncbi_taxonomy_id	420246
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Nanobody
Molecular weight formula_weight	12919.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

QVQLVETGGGLVQPGGSLRLSCGASGSIFNMYAMGWYRQAPGKRREVVARIATDDSTMYPDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCYYQRTVMSQPYWGQGTQVTVS

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Translocating peptide
Molecular weight formula_weight	6024.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAKKTAIAIAVALAGFATVASYAQYEDGCSGELERQHTFAGGARSISGDGDSPHSYHSG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Green fluorescent protein
Molecular weight formula_weight	26813.1 kDa
Mutation mutation	Q80R,F99S,M153T,V163A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFXVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK

Source Source

Source organism organism	Aequorea victoria
Common name common_name	Jellyfish
NCBI taxonomy ID ncbi_taxonomy_id	6100
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Nanobody
Molecular weight formula_weight	12368.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

VALVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSAGDRSSYEDSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCNVNVGFEYWGQGTQVTVS

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
Molecular weight formula_weight	749.0 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6itcA01
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	6itcA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1440 — Pre-protein croslinking domain of SecA
Homologous superfamily homologous superfamily	10 — SecA, preprotein cross-linking domain

Domain ID domain_id	6itcA03
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	6itcA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3060 — Helical scaffold and wing domains of SecA
Homologous superfamily homologous superfamily	10 — Helical scaffold and wing domains of SecA

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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	1

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

Resolution resolution	3.45 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	130153

Structure of a substrate engaged SecA-SecY protein translocation machine

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

Protein translocase subunit SecA

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 translocase subunit SecY

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 translocase subunit SecE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Green fluorescent protein

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

6itc__assembly_1__model_1

6itc__assembly_1__model_1 | I(q)

6itc__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 (11)

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 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)