SAXSdb — 8zkp

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

Siderophore exporter MmpL5

Mycobacterium tuberculosis H37Rv

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Siderophore export accessory protein MmpS5 × 3 （P9WJS7） Meromycolate extension acyl carrier protein × 3 （A0R0B3） CARDIOLIPIN × 6 (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 6 N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MMPL5_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–964； UniProt 1–964 Author chain B； PDBConstruct 1–964； UniProt 1–964 Author chain E； PDBConstruct 1–964； UniProt 1–964

Siderophore export accessory protein MmpS5

Mycobacterium tuberculosis H37Rv

UniProt P9WJS7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Siderophore exporter MmpL5 × 3 （P9WJV1） Meromycolate extension acyl carrier protein × 3 （A0R0B3） CARDIOLIPIN × 6 (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 6 N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MMPS5_MYCTU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–142； UniProt 1–142 Author chain F； PDBConstruct 1–142； UniProt 1–142 Author chain G； PDBConstruct 1–142； UniProt 1–142

Meromycolate extension acyl carrier protein

Mycolicibacterium smegmatis MC2 155

UniProt A0R0B3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Siderophore exporter MmpL5 × 3 （P9WJV1） Siderophore export accessory protein MmpS5 × 3 （P9WJS7） CARDIOLIPIN × 6 (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 6 N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACPM_MYCS2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–99； UniProt 1–99 Author chain H； PDBConstruct 1–99； UniProt 1–99 Author chain I； PDBConstruct 1–99； UniProt 1–99

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	8zkp
Deposition date deposition_date	2024-05-17
Structure title title	Cryo-EM structure of the efflux transporter MmpL5/MmpS5 from Mycobacterium tuberculosis, C3 symmetry
Keywords keywords	membrane transporter, MEMBRANE PROTEIN; MEMBRANE 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.

8zkp__assembly_1__model_1

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

Download this curve (.dat)

8zkp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8zkp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.01 Å
Rg (electron density)	44.53 Å
Total Rg	44.68 Å
Atom count	21087
Residues	2667
Excluded volume	385920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8zkp__assembly_1__model_1`	nonameric （9）	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	Siderophore exporter MmpL5
Molecular weight formula_weight	104874.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E
Atom count atom_count	21087

MIVQRTAAPTGSVPPDRHAARPFIPRMIRTFAVPIILGWLVTIAVLNVTVPQLETVGQIQAVSMSPDAAPSMISMKHIGKVFEEGDSDSAAMIVLEGQRPLGDAAHAFYDQMIGRLQADTTHVQSLQDFWGDPLTATGAQSSDGKAAYVQVKLAGNQGESLANESVEAVKTIVERLAPPPGVKVYVTGSAALVADQQQAGDRSLQVIEAVTFTVIIVMLLLVYRSIITSAIMLTMVVLGLLATRGGVAFLGFHRIIGLSTFATNLLVVLAIAAATDYAIFLIGRYQEARGLGQDRESAYYTMFGGTAHVVLGSGLTIAGATFCLSFTRLPYFQTLGVPLAIGMVIVVAAALTLGPAIIAVTSRFGKLLEPKRMARVRGWRKVGAAIVRWPGPILVGAVALALVGLLTLPGYRTNYNDRNYLPADLPANEGYAAAERHFSQARMNPEVLMVESDHDMRNSADFLVINKIAKAIFAVEGISRVQAITRPDGKPIEHTSIPFLISMQGTSQKLTEKYNQDLTARMLEQVNDIQSNIDQMERMHSLTQQMADVTHEMVIQMTGMVVDVEELRNHIADFDDFFRPIRSYFYWEKHCYDIPVCWSLRSVFDTLDGIDVMTEDINNLLPLMQRLDTLMPQLTAMMPEMIQTMKSMKAQMLSMHSTQEGLQDQMAAMQEDSAAMGEAFDASRNDDSFYLPPEVFDNPDFQRGLEQFLSPDGHAVRFIISHEGDPMSQAGIARIAKIKTAAKEAIKGTPLEGSAIYLGGTAAMFKDLSDGNTYDLMIAGISALCLIFIIMLITTRSVVAAAVIVGTVVLSLGASFGLSVLIWQHILGIELHWLVLAMAVIILLAVGADYNLLLVARLKEEIHAGINTGIIRAMGGSGSVVTAAGLVFAFTMMSFAVSELTVMAQVGTTIGMGLLFDTLIVRSFMTPSIAALLGKWFWWPQVVRQRPIPQPWPSPASARTFALV

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 2 Entity 2 polymer

Description description	Siderophore export accessory protein MmpS5
Molecular weight formula_weight	15261.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,C,G

MIGTLKRAWIPLLILVVVAIAGFTVQRIRTFFGSEGILVTPKVFADDPEPFDPKVVEYEVSGSGSYVNINYLDLDAKPQRIDGAALPWSLTLKTTAPSAAPNILAQGDGTSITCRITVDGEVKDERTATGVDALTYCFVKSA

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 3 Entity 3 polymer

Description description	Meromycolate extension acyl carrier protein
Molecular weight formula_weight	10743.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,D,I

MAATQEEIIAGLAEIIEEVTGIEPSEVTPEKSFVDDLDIDSLSMVEIAVQTEDKYGVKIPDEDLAGLRTVGDVVAYIQKLEEENPEAAAALREKFAADQ

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Mycolicibacterium smegmatis MC2 155

Entity 4 Entity 4 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
Molecular weight formula_weight	720.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
Molecular weight formula_weight	358.3 kDa
Source method src_method	syn
Copy count entity_count	3

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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	2.64 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	83178

Cryo-EM structure of the efflux transporter MmpL5/MmpS5 from Mycobacterium tuberculosis, C3 symmetry

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

Siderophore exporter MmpL5

State in the Current Structure

Other States of the Same Protein in the Database

Siderophore export accessory protein MmpS5

State in the Current Structure

Other States of the Same Protein in the Database

Meromycolate extension acyl carrier 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

8zkp__assembly_1__model_1

8zkp__assembly_1__model_1 | I(q)

8zkp__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 (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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)

Cryo-EM structure of the efflux transporter MmpL5/MmpS5 from Mycobacterium tuberculosis, C3 symmetry

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

Siderophore exporter MmpL5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Siderophore export accessory protein MmpS5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Meromycolate extension acyl carrier 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

8zkp__assembly_1__model_1

8zkp__assembly_1__model_1 | I(q)

8zkp__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 (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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)