SAXSdb — 5mg3

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

Protein translocase subunit SecY

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） Protein translocase subunit SecD × 1 （P0AG90） Protein translocase subunit SecF × 1 （P0AG93） Membrane protein insertase YidC × 1 （P25714）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECY_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain Y； PDBConstruct 16–458； UniProt 1–443

Protein translocase subunit SecE

Escherichia coli

UniProt P0AG96

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein translocase subunit SecY × 1 （P0AGA2） Protein-export membrane protein SecG × 1 （P0AG99） Protein translocase subunit SecD × 1 （P0AG90） Protein translocase subunit SecF × 1 （P0AG93） Membrane protein insertase YidC × 1 （P25714）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECE_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 16–140； UniProt 3–127

Protein-export membrane protein SecG

Escherichia coli

UniProt P0AG99

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein translocase subunit SecY × 1 （P0AGA2） Protein translocase subunit SecE × 1 （P0AG96） Protein translocase subunit SecD × 1 （P0AG90） Protein translocase subunit SecF × 1 （P0AG93） Membrane protein insertase YidC × 1 （P25714）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECG_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 27–136； UniProt 1–110

Protein translocase subunit SecD

Escherichia coli

UniProt P0AG90

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein translocase subunit SecY × 1 （P0AGA2） Protein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） Protein translocase subunit SecF × 1 （P0AG93） Membrane protein insertase YidC × 1 （P25714）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECD_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 9–622； UniProt 2–615

Protein translocase subunit SecF

Escherichia coli

UniProt P0AG93

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein translocase subunit SecY × 1 （P0AGA2） Protein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） Protein translocase subunit SecD × 1 （P0AG90） Membrane protein insertase YidC × 1 （P25714）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECF_ECOLI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–323； UniProt 1–323

Membrane protein insertase YidC

Escherichia coli

UniProt P25714

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein translocase subunit SecY × 1 （P0AGA2） Protein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） Protein translocase subunit SecD × 1 （P0AG90） Protein translocase subunit SecF × 1 （P0AG93）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YIDC_ECOLI
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain C； PDBConstruct 7–553； UniProt 2–548

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	5mg3
Deposition date deposition_date	2016-11-20
Structure title title	EM fitted model of bacterial holo-translocon
Keywords keywords	holotranslocon, membrane protein insertion machinery, chaperone, protein secretion; CHAPERONE
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.

5mg3__assembly_1__model_1

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

Download this curve (.dat)

5mg3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5mg3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.04 Å
Rg (electron density)	38.07 Å
Total Rg	38.55 Å
Atom count	26650
Residues	1698
Excluded volume	237980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5mg3__assembly_1__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	Protein translocase subunit SecY
Molecular weight formula_weight	50410.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y
Atom count atom_count	26650

VWNCERITISHRKQTMAKQPGLDFQSAKGGLGELKRRLLFVIGALIVFRIGSFIPIPGIDAAVLAKLLEQQRGTIIEMFNMFSGGALSRASIFALGIMPYISASIIIQLLTVVHPTLAEIKKEGESGRRKISQYTRYGTLVLAIFQSIGIATGLPNMPGMQGLVINPGFAFYFTAVVSLVTGTMFLMWLGEQITERGIGNGISIIIFAGIVAGLPPAIAHTIEQARQGDLHFLVLLLVAVLVFAVTFFVVFVERGQRRIVVNYAKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSIILFPATIASWFGGGTGWNWLTTISLYLQPGQPLYVLLYASAIIFFCFFYTALVFNPRETADNLKKSGAFVPGIRPGEQTAKYIDKVMTRLTLVGALYITFICLIPEFMRDAMKVPFYFGGTSLLIVVVVIMDFMAQVQTLMMSSQYESALKKANLKGYGR

Source Source

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

Entity 2 Entity 2 polymer

Description description	Protein translocase subunit SecE
Molecular weight formula_weight	15248.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MHHHHHHDDDDKAMGANTEAQGSGRGLEAMKWVVVVALLLVAIVGNYLYRDIMLPLRALAVVILIAAAGGVALLTTKGKATVAFAREARTEVRKVIWPTRQETLHTTLIVAAVTAVMSLILWGLDGILVRLVSFITGLRF

Source Source

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

Entity 3 Entity 3 polymer

Description description	Protein-export membrane protein SecG
Molecular weight formula_weight	14326.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

VGTGWYSGSPGILYHWPEVLRIQELIMYEALLVVFLIVAIGLVGLIMLQQGKGADMGASFGAGASATLFGSSGSGNFMTRMTALLATLFFIISLVLGNINSNKTNKGSEWENLSAPAKTEQTQPAAPAKPTSDIPN

Source Source

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

Entity 4 Entity 4 polymer

Description description	Protein translocase subunit SecD
Molecular weight formula_weight	67688.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MHHHHHHMLNRYPLWKYVMLIVVIVIGLLYALPNLFGEDPAVQITGARGVAASEQTLIQVQKTLQEEKITAKSVALEEGAILARFDSTDTQLRAREALMGVMGDKYVVALNLAPATPRWLAAIHAEPMKLGLDLRGGVHFLMEVDMDTVLGKLQEQNIDSLRSDLREKGIPYTTVRKENNYGLSITFRDAKARDEAIAYLSKRHPDLVISSQGSNQLRAVMSDARLSEAREYAVQQNINILRNRVNQLGVAEPVVQRQGADRIVVELPGIQDTARAKEILGATATLEFRLVNTNVDQAAAASGRVPGDSEVKQTREGQPVVLYKRVILTGDHITDSTSSQDEYNQPQVNISLDSAGGNIMSNFTKDNIGKPMATLFVEYKDSGKKDANGRAVLVKQEEVINIANIQSRLGNSFRITGINNPNEARQLSLLLRAGALIAPIQIVEERTIGPTLGMQNIEQGLEACLAGLLVSILFMIIFYKKFGLIATSALIANLILIVGIMSLLPGATLSMPGIAGIVLTLAVAVDANVLINERIKEELSNGRTVQQAIDEGYRGAFSSIFDANITTLIKVIILYAVGTGAIKGFAITTGIGVATSMFTAIVGTRAIVNLLYGGKRVKKLSI

Source Source

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

Entity 5 Entity 5 polymer

Description description	Protein translocase subunit SecF
Molecular weight formula_weight	35413.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MAQEYTVEQLNHGRKVYDFMRWDYWAFGISGLLLIAAIVIMGVRGFNWGLDFTGGTVIEITLEKPAEIDVMRDALQKAGFEEPMLQNFGSSHDIMVRMPPAEGETGGQVLGSQVLKVINESTNQNAAVKRIEFVGPSVGADLAQTGAMALMAALLSILVYVGFRFEWRLAAGVVIALAHDVIITLGILSLFHIEIDLTIVASLMSVIGYSLNDSIVVSDRIRENFRKIRRGTPYEIFNVSLTQTLHRTLITSGTTLMVILMLYLFGGPVLEGFSLTMLIGVSIGTASSIYVASALALKLGMKREHMLQQKVEKEGADQPSILP

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	Membrane protein insertase YidC
Molecular weight formula_weight	62658.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MDPSSRDSQRNLLVIALLFVSFMIWQAWEQDKNPQPQAQQTTQTTTTAAGSAADQGVPASGQGKLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPMTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLPPHLDTGSSNFALHTFRGAAYSTPDAAYAAYAFDTIADNENLNISSKGGWVAMLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAMNSTLWVGPEIQDKMAAVAPHLDLTVDYGWLWFISQPLFKLLKWIHSFVGNWGFSIIIITFIVRGIMYPLTKAQYTSMAKMRMLQPKIQAMRERLGDDKQRISQEMMALYKAEKVNPLGGCFPLLIQMPIFLALYYMLMGSVELRQAPFALWIHDLSAQDPYYILPILMGVTMFFIQKMSPTTVTDPMQQKIMTFMPVIFTVFFLWFPSGLVLYYIVSNLVTIIQQQLIYRGLEKRGLHSREKKKSHHHHHH

Source Source

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

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Resolution resolution	14.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	53648

EM fitted model of bacterial holo-translocon

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

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

Protein-export membrane protein SecG

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 SecD

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 SecF

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Membrane protein insertase YidC

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

5mg3__assembly_1__model_1

5mg3__assembly_1__model_1 | I(q)

5mg3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

Source Source

7. Citations (1)