SAXSdb — 7b9s

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

EccE5

Mycobacterium xenopi RIVM700367

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 30	EccD5 × 12 （I0RSS8） EccC5 × 6 （I0RZI0） EccB5 × 6 （I0RZH9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I0RST0_MYCXE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 4； PDBConstruct 1–400； UniProt 1–400 Author chain E； PDBConstruct 1–400； UniProt 1–400 Author chain H； PDBConstruct 1–400； UniProt 1–400 Author chain M； PDBConstruct 1–400； UniProt 1–400 Author chain R； PDBConstruct 1–400； UniProt 1–400 Author chain Y； PDBConstruct 1–400； UniProt 1–400

EccD5

Mycobacterium xenopi RIVM700367

UniProt I0RSS8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 30	EccE5 × 6 （I0RST0） EccC5 × 6 （I0RZI0） EccB5 × 6 （I0RZH9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I0RSS8_MYCXE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 3； PDBConstruct 1–502； UniProt 1–502 Author chain 5； PDBConstruct 1–502； UniProt 1–502 Author chain D； PDBConstruct 1–502； UniProt 1–502 Author chain G； PDBConstruct 1–502； UniProt 1–502 Author chain I； PDBConstruct 1–502； UniProt 1–502 Author chain L； PDBConstruct 1–502； UniProt 1–502 Author chain N； PDBConstruct 1–502； UniProt 1–502 Author chain Q； PDBConstruct 1–502； UniProt 1–502 Author chain S； PDBConstruct 1–502； UniProt 1–502 Author chain W； PDBConstruct 1–502； UniProt 1–502 Author chain X； PDBConstruct 1–502； UniProt 1–502 Author chain Z； PDBConstruct 1–502； UniProt 1–502

EccC5

Mycobacterium xenopi RIVM700367

UniProt I0RZI0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 30	EccE5 × 6 （I0RST0） EccD5 × 12 （I0RSS8） EccB5 × 6 （I0RZH9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I0RZI0_MYCXE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 2； PDBConstruct 1–1392； UniProt 1–1392 Author chain C； PDBConstruct 1–1392； UniProt 1–1392 Author chain F； PDBConstruct 1–1392； UniProt 1–1392 Author chain K； PDBConstruct 1–1392； UniProt 1–1392 Author chain P； PDBConstruct 1–1392； UniProt 1–1392 Author chain V； PDBConstruct 1–1392； UniProt 1–1392

EccB5

Mycobacterium xenopi RIVM700367

UniProt I0RZH9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 30	EccE5 × 6 （I0RST0） EccD5 × 12 （I0RSS8） EccC5 × 6 （I0RZI0）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I0RZH9_MYCXE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain 1； PDBConstruct 1–506； UniProt 1–506 Author chain A； PDBConstruct 1–506； UniProt 1–506 Author chain B； PDBConstruct 1–506； UniProt 1–506 Author chain J； PDBConstruct 1–506； UniProt 1–506 Author chain O； PDBConstruct 1–506； UniProt 1–506 Author chain T； PDBConstruct 1–506； UniProt 1–506

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	7b9s
Deposition date deposition_date	2020-12-14
Structure title title	Structure of the mycobacterial ESX-5 Type VII Secretion System hexameric pore complex
Keywords keywords	Mycobacterial ESX-5 Type VII Secretion System, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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.

7b9s__assembly_1__model_1

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

Download this curve (.dat)

7b9s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7b9s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	81.29 Å
Rg (electron density)	80.75 Å
Total Rg	80.61 Å
Atom count	72030
Residues	9426
Excluded volume	1302200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7b9s__assembly_1__model_1`	30-meric （30）	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 (4)

Entity 1 Entity 1 polymer

Description description	EccE5
Molecular weight formula_weight	44469.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,H,M,R,Y,4
Atom count atom_count	72030

MRAQRRFGLDLSWPRLTGVFLIDVAVLALVSHLPDAWQANHIAWWTGVGVAVLVTIVAVVTYRRTPLACALVARVLDRFVDPEMTLTEGCTPALDHQRRFGHDVVGIREYQGQLVAVVTVEGHEEAPSGRHRNRDAAPAWLPVEAVAARLRQFDVRLDAIDIVSVGTRRTSGRDDVSDVGVDDTGPVDARQPLDEHHTWLVLRMDPQRNVAAVAARDSVAATLAAATERLAHDLNGRRWTARPLTSSEIDDMDATVLAGLQPAHVRPRRRRLKYKQPEGYKEFVTSFWVSPRDITSETLERLWLPDTEATAVTVRLRPRHGGVEVSAWVRYHSSRRLRRSVWGGLNRLTGRQLDAVCASMPVPTRRPRLVVPARELHDGEELAVLVGQAPAPSPSPAAAR

Source Source

Source organism organism	Mycobacterium xenopi RIVM700367
NCBI taxonomy ID ncbi_taxonomy_id	1150591
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 2 Entity 2 polymer

Description description	EccD5
Molecular weight formula_weight	53399.2 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,D,I,G,N,L,S,Q,Z,W,5,3

MTAIVEAPQPGAEAIASPQAAVVAIMAADVQIAVVLDAHAPISVMIDPLLKVVNTRLRELGVAPLEAKGRGRWMLCLVDGTPLRPNLSLTEQEVYDGDRLWLKFLEDTEHRSEVIEHISTAVATNLSKRFAPIDPVVAVQVGATMVAVGVLLGSALLGWWRWQHESWLPAPFAAVIAVLVLTVATMILARSKTVPDRRVGDILLLSGLVPLAVAIAATAPGPVGAPHAVLGFGVFGVAAMLVMRFTGRRLGVYTALVTLCAAATAAGLARMVLLTSAVTLLTCVLLACVLMYHGAPALSRWLSGIRLPVFPSATSRWVFEARPDLPTTVVVSGGGQPTLEGPASVRDVLLRAERARSFLTGLLVGLGVLTVVCLAGLCDPHAGRRWLPLLLAAFTFGFLILRGRSYVDRWQAITLAATAVLIIAAVAVRYVLVSGSPAVLSAGVAVLVLLPAAGLTAAAVVPNTIYSPLFRKIVEWIEYLCLMPIFPLALWLMNVYEAIRYR

Source Source

Source organism organism	Mycobacterium xenopi RIVM700367
NCBI taxonomy ID ncbi_taxonomy_id	1150591
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 3 Entity 3 polymer

Description description	EccC5
Molecular weight formula_weight	152946.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,K,P,V,2

MKQGFARPTPERAPVVKPENIVLPTPLSVPPPEGKPWWLVVVGVLVVGLLVGMVGMTVASGSRLFLGAGAIFPIFMIGGVAMMMFGGRFGGQQQMSRPKLDAMRAQFMLMLDMLRETAQESADSMDANYRWFHPAPTTLAAAVGSSRMWERQPDGKDLNFGVVRVGVGMTRPEVTWGEPQNMPTDIELEPVTGKALQEFGRYQSVVYNLPKMVSLLVEPWYSLVGEREQVLGLTRAIICQLAFSHGPDHVQMIVVTSDPDRWDWVKWIPHFGDPRRRDAAGNARMVYTSVREFATEQAELFAGRGSFTPRHASSSAETPTPHHVIISDIEDPQWEYVISSEGVDGVTFFDLTGSPLWTGAPQRVLRFTDSAGVIETLPRDRDTWMVIDDNAWFFALADQMSEADAEQFAHQMAHWRLAEAYEEIGQRVVQLGARDILSYYGIDDAGEIDFNTLWSGSGRRDLLSRSRLRIPFGNRADNGELLFLDMKSLDEGGDGPHGVMSGTTGSGKSSLVRTVIASLMLAHPPEELQFVLADLKGGSAVKPFDGVPHVSRIITDLEDDQALMERFLEAMWGEIARRKEICFSAGVDGAKEYNELRARMKARGEDMPPLPMLVVVIDEFYEWFRIMPTAVDVLDSIGRQGRAYWVHLMMASQTIESRAEKLMENMGYRLVLKAQTAGAAQAAGVPNAVNLPSQAGLGYFRKSGDEIIRFQAEYLWRDYRRGSSYDGEEQAPLTHSVDYIRPQLFTTAFAPLEVSVSGPDGQSALPQVVDGEAVNGHRGGDDVDEEEEALRTPKVGTVIIDQLRQIDFEPYRLWHPPLDVPVPIDELVNRFLGRPWQQDYGTAKNLVFPIGIIDRPYKHDQPPWTVDTSGAGANVLILGAGGAGKTTALQTLICAAALTHTPEQVQFYCLAYSGTALTTVANLPHVGGVSGPTDPYGVRRTVAEVLGLVRDRKRSFLEYDVPSMEVFRRRKFGGEPGGVPDDGFGDVYLVIDNYRALAEENEVLIEQVNQIINQGPSFGVHVVATADRESELRPPVRSGFGSRVELRLAAVEDAKLVRSRFAKDVPPKPGRGMVAVNYVRLDSDPQAGLHTLVARPALGSTPDAVFESDSVAAAVRQVAAGEARPVRRLPARFGLDQLRQVAAADRRQGVGAGGIAWAISELDLQPVYLNFADNAHLMVTGRRECGRTTTLATIMSEIGRIYAPGASTAPPTSRPSAQVWLVDPRRQLLTVLGSDYVEKFAYNLDGVAAMMDDLAAALARREPPPGLSAEELLSRSWWSGPEIFLIIDDIQQLPPGFDSPLHKAAPWVTRAADVGLHVFVTRTFGGWSSAGSDPILRALHQANAPLLVMDADPDEGFIRGKMKGGPLPRGRGLLMAEDTGVFVQVAATDLRR

Source Source

Source organism organism	Mycobacterium xenopi RIVM700367
NCBI taxonomy ID ncbi_taxonomy_id	1150591
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 4 Entity 4 polymer

Description description	EccB5
Molecular weight formula_weight	53226.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,J,O,T,1

MPSEQRGQHRSGYGLGLSTRTQVTGYQFLARRTAMALTRWRVRMEVEPGRRQVLAVVASVSAAGVICLGALLWSFISPSGQMGESPIIADRDSGALYVRVGDTLYPALNLASARLIAGRAENPHKVRSSQIAEQPHGPMVGIPGAPSDISPTSPASSSWLVCDAVTAAQGVGAPASVTVTVIDGTPDLSGRRHVLSGSDAVVLRYGNDTWVIRQGRRSRIDAANRAVLLPLGLTPEQVKQASPMSRALYDALPVGPELAVPKVPDAGKPANFPGAPAPVGAVLVTPQISGPQQYSVVLPDGVQTISPIVAQILQNAGTPAGSMPVVVAPATLARMPVVHGLDLSAYPDSPLNVVNMKENPATCWWWEKTAGEERARTQVVSGPTVPIATSDTNKVVSLVKADNTGREADRVYYGPNYANFVVVTGNDPAASTAESLWLLSKSGVRFGVDNSREARTALGLTSTPSPAPWVALRLLAPGPMLSRADALVRHDTLPTDTNPAELAVPK

Source Source

Source organism organism	Mycobacterium xenopi RIVM700367
NCBI taxonomy ID ncbi_taxonomy_id	1150591
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

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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	triclinic

Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	121974

Structure of the mycobacterial ESX-5 Type VII Secretion System hexameric pore complex

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

EccE5

State in the Current Structure

Other States of the Same Protein in the Database

EccD5

State in the Current Structure

Other States of the Same Protein in the Database

EccC5

State in the Current Structure

Other States of the Same Protein in the Database

EccB5

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7b9s__assembly_1__model_1

7b9s__assembly_1__model_1 | I(q)

7b9s__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 (4)

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

7. Citations (1)

Structure of the mycobacterial ESX-5 Type VII Secretion System hexameric pore complex

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

EccE5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

EccD5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

EccC5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

EccB5

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

7b9s__assembly_1__model_1

7b9s__assembly_1__model_1 | I(q)

7b9s__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 (4)

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

7. Citations (1)