SAXSdb — 9qks

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

ESX secretion system protein YukD

Bacillus subtilis subsp. subtilis str. 168

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	ESX secretion system protein YukC × 2 （P71070） ESX secretion system protein YukB,Green fluorescent protein × 2 （C0SPA7,P42212）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YUKD_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–81； UniProt 1–79

ESX secretion system protein YukC

Bacillus subtilis subsp. subtilis str. 168

UniProt P71070

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	ESX secretion system protein YukD × 1 （P71071） ESX secretion system protein YukB,Green fluorescent protein × 2 （C0SPA7,P42212）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YUKC_BACSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–451； UniProt 1–451 Author chain D； PDBConstruct 1–451； UniProt 1–451

ESX secretion system protein YukB,Green fluorescent protein

Bacillus subtilis subsp. subtilis str. 168

UniProt C0SPA7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	ESX secretion system protein YukD × 1 （P71071） ESX secretion system protein YukC × 2 （P71070）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YUKB_BACSU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 13–973； UniProt 2–962 Author chain H； PDBConstruct 13–973； UniProt 2–962

ESX secretion system protein YukB,Green fluorescent protein

Bacillus subtilis subsp. subtilis str. 168

UniProt P42212

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	ESX secretion system protein YukD × 1 （P71071） ESX secretion system protein YukC × 2 （P71070）	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	3
Chains and sequence ranges	Author chain G； PDBConstruct 995–1218； UniProt 7–230 Author chain H； PDBConstruct 995–1218； UniProt 7–230

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	9qks
Deposition date deposition_date	2025-03-20
Structure title title	B subtilis Type VIIb Core Unit (T7bCU) + DUF
Keywords keywords	T7SS, Type VII Secretion System, T7bCU, 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.

9qks__assembly_1__model_1

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

Download this curve (.dat)

9qks__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qks__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.66 Å
Rg (electron density)	41.11 Å
Total Rg	41.49 Å
Atom count	11940
Residues	1441
Excluded volume	212550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qks__assembly_1__model_1`	pentameric （5）	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 (3)

Entity 1 Entity 1 polymer

Description description	ESX secretion system protein YukD
Molecular weight formula_weight	9277.7 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	11940

MGMYIDITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEIL

Source Source

Source organism organism	Bacillus subtilis subsp. subtilis str. 168
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	ESX secretion system protein YukC
Molecular weight formula_weight	53225.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MSGEQKSYLENQLEAVAEKTDAGYTFTFQREKIKLLDGLEANVIKDINPFFHKEIDVTDDEVIITIQPPSSYKAFRFMKAKDKKSKWQFAYQLVQAVQQHNLSRLNLIVAPENIVFDKGLTPYFLHYGVKESIPPYERDEERVWQELKAAAALAVDGAFAFEDYLKFNETLTFSAEAKAILDAESYDDLLELIQTHIDELEAKAKTYIHIPRKKWNIQRYIGLGLIVLLVPALIYSMYALFFAQPKHQAIVDSNRAFLNKQYSEVISTLSKYDAESLPESVQYQLATSYVEVENLGSAKTKNIENNLVTLQSDPQHFLYWIDYGRGEYKEAISIGRKLEYNDYIYFALAKYKQQLLSEDTNDEDIQKELDSVNSELEKAQKERQENKQSNSETSLVDTSEEQTQTDEEKQAEEKAAEEKAAAEEKAKKEEQKEKEDEKKETEKKDEKKDDKDYKDDDDK

Source Source

Source organism organism	Bacillus subtilis subsp. subtilis str. 168
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	ESX secretion system protein YukB,Green fluorescent protein
Molecular weight formula_weight	143109.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H

MLPFGRKGVRHLSLLWVFYQNNVQKLNLSNLPSSHPVTIGPDVKDSVTISTIPFNSGVISLKRKESGGQYEVFLGNDCLGTIETDISFTLQTDQQDIRLILTGSEPEKSVYFTGNRDEIVCSSEKTNADIYLNPQDFAFAEQSTFSLLRAGGSWSVRPESGTIFLNGEKINANTPLKPGDEIFWNFTQMRVTEQDLLEIVHYAQFETALTETVKPSTEMQKKYPQYRRTPRMVYDLPDDRVSFSFPSQESDQTNRGLWLVILPPLVMLIVMGVVAIIQPRGIFILVSLAMFMMTLITSTVQYFRDKNQRKKREEKRERVYKLYLDNKRKELQALAEKQKQVLEFHFPSFEQMKYLTSEISDRIWEKSLESKDYLQLRLGTGTVPSSYEINMSGGDLANRDIDDLMEKSQHMQRVYKDIRNAPVTVDLAEGPMGLVGKSQIVKNEIHQLIGQLSFFNSYHDLRFVFIFHEEEYKDWEWMKWLPQFQMPHIYAKGFIYNEQTRDQLLSSLYELIRERDLEDDKEKLQFKPHFVFVITNQQLISEHVILEYLEGQHEHLGISTIVAAETKESLSENITTLVRYINEHEGDILIQKKKAVRIPFRLDHHQREDNERFSRTLRTLNHQVGITNSIPETVSFLELFHAKEVKEIGIQQRWLTSESSKSLSVPIGYKGKDDIVYLNLHEKAHGPHGLLAGTTGSGKSEFLQTYILSLAVHFHPHEAAFLLIDYKGGGMAQPFRNIPHLLGTITNIEGSKNFSMRALASIKSELKKRQRLFDQYQVNHINDYTKLYKQGKAEVAMPHLFLISDEFAELKSEEPDFIRELVSAARIGRSLGVHLILATQKPGGIIDDQIWSNSRFKVALKVQDATDSKEILKNSDAANITVTGRGYLQVGNNEVYELFQSAWSGAPYLEEVYGTEDEIAIVTDTGLIPLSEVDTEDNAKKDVQTEIEAVVDEIERIQDEMGIEKLPSPWLPPGAGGLVPRGSGGSGSVDSTESLFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTITFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITGGSGGSGSRGRSGSGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKKG

Source Source

Source organism organism	Bacillus subtilis subsp. subtilis str. 168
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli BL21(DE3)

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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	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	303198

B subtilis Type VIIb Core Unit (T7bCU) + DUF

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

ESX secretion system protein YukD

State in the Current Structure

Other States of the Same Protein in the Database

ESX secretion system protein YukC

State in the Current Structure

Other States of the Same Protein in the Database

ESX secretion system protein YukB,Green fluorescent protein

State in the Current Structure

Other States of the Same Protein in the Database

ESX secretion system protein YukB,Green fluorescent protein

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

9qks__assembly_1__model_1

9qks__assembly_1__model_1 | I(q)

9qks__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 (3)

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

7. Citations (1)

B subtilis Type VIIb Core Unit (T7bCU) + DUF

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

ESX secretion system protein YukD

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ESX secretion system protein YukC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ESX secretion system protein YukB,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

ESX secretion system protein YukB,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

9qks__assembly_1__model_1

9qks__assembly_1__model_1 | I(q)

9qks__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 (3)

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

7. Citations (1)