SAXSdb — 7vly

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

Mannose/fructose/sorbose family PTS transporter subunit IIC

Listeria monocytogenes

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	PTS mannose family transporter subunit IID × 3 （A0A1E8EBU8） Bacteriocin pediocin PA-1 × 3 （P29430） alpha-D-mannopyranose × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S5LAD9_LISMN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–268； UniProt 1–268 Author chain F； PDBConstruct 1–268； UniProt 1–268 Author chain Y； PDBConstruct 1–268； UniProt 1–268

PTS mannose family transporter subunit IID

Listeria monocytogenes

UniProt A0A1E8EBU8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Mannose/fructose/sorbose family PTS transporter subunit IIC × 3 （S5LAD9） Bacteriocin pediocin PA-1 × 3 （P29430） alpha-D-mannopyranose × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A1E8EBU8_LISMN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–303； UniProt 1–303 Author chain G； PDBConstruct 1–303； UniProt 1–303 Author chain Z； PDBConstruct 1–303； UniProt 1–303

Bacteriocin pediocin PA-1

Pediococcus acidilactici

UniProt P29430

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Mannose/fructose/sorbose family PTS transporter subunit IIC × 3 （S5LAD9） PTS mannose family transporter subunit IID × 3 （A0A1E8EBU8） alpha-D-mannopyranose × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPA1_PEDAC
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 4–47； UniProt 19–62 Author chain E； PDBConstruct 4–47； UniProt 19–62 Author chain H； PDBConstruct 4–47； UniProt 19–62

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	7vly
Deposition date deposition_date	2021-10-05
Structure title title	Cryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1
Keywords keywords	;antimicrobial peptides; bacteriocins; pediocin PA-1; pediocin-like/class IIa bacteriocins; antibiotic resistance; mannose phosphotransferase; man-PTS, 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.

7vly__assembly_1__model_1

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

Download this curve (.dat)

7vly__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7vly__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.64 Å
Rg (electron density)	41.15 Å
Total Rg	41.50 Å
Atom count	13317
Residues	1773
Excluded volume	243250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7vly__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 (5)

Entity 1 Entity 1 polymer

Description description	Mannose/fructose/sorbose family PTS transporter subunit IIC
Molecular weight formula_weight	27377.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,C,F
Atom count atom_count	13347

MSVISIILVVLIAFLAGIEGILDEFQFHQPLIACTLIGLVTGNLTACIILGGTLQMIALGWANIGAAVAPDAALASVASAIILVLGGQGVAGIPSAIAIAIPLAVAGLFLTMIVRTLAVPIVHLMDRAAEKGNIRSVEWLHISAICMQGIRIAIPAAALLFIPADSVQSFLEAMPAWLTDGMAIGGGMVVAVGYALVINMMATKEVWPFFVIGFVVAAISQLTLIAIGALGVALALIYLNLSKMGGGNSNGGGGGNSRDPLGDILNDY

Source Source

Source organism organism	Listeria monocytogenes
NCBI taxonomy ID ncbi_taxonomy_id	1639
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PTS mannose family transporter subunit IID
Molecular weight formula_weight	33402.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z,D,G

MAEKIELSKRDRLRVAWRSTFIQGSWNYERMQNGGWAFSMIPAIKKLYKTKEDRSSALKRHLEFFNTHPYIASPILGVTLALEEERANGAEVDDVAIQGVKVGMMGPLAGVGDPVFWFTIRPMLGALGASLALSGNILGPILFFVAWNVIRWGFMWYTQEFGYKAGSKITDDLSGGLLQDITKGASILGMFVLAALVQRWVNIQFAPIISKVKLDEGAYIDWSHLPQGAQGIKTALQQQQAGLALSEIKVTTLQNNLDNLIPGLAAVALTFLCMWLLKKKISPIIIILGLFVVGIVGHLIGLL

Source Source

Source organism organism	Listeria monocytogenes
NCBI taxonomy ID ncbi_taxonomy_id	1639
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Bacteriocin pediocin PA-1
Molecular weight formula_weight	5001.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,H

PHMKYYGNGVTCGKHSCSVDWGKATTCIINNGAMAWATGGHQGNHKC

Source Source

Source organism organism	Pediococcus acidilactici
NCBI taxonomy ID ncbi_taxonomy_id	1254
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	30

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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	2.45 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	659531

Cryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1

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

Mannose/fructose/sorbose family PTS transporter subunit IIC

State in the Current Structure

Other States of the Same Protein in the Database

PTS mannose family transporter subunit IID

State in the Current Structure

Other States of the Same Protein in the Database

Bacteriocin pediocin PA-1

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

7vly__assembly_1__model_1

7vly__assembly_1__model_1 | I(q)

7vly__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 (5)

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 water

7. Citations (1)

Cryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1

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

Mannose/fructose/sorbose family PTS transporter subunit IIC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PTS mannose family transporter subunit IID

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Bacteriocin pediocin PA-1

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

7vly__assembly_1__model_1

7vly__assembly_1__model_1 | I(q)

7vly__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 (5)

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 water

7. Citations (1)