9vfr

Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1

Method: ELECTRON MICROSCOPY Dmax: 114.2 Å Quality: GOOD

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

Genome polyprotein

OrganismNot specified

UniProt A0A222NWY2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 300 PDB declaration: 300-meric(300) Consistent with protein copy count Chain A; UniProt 1–305 Not recorded Genome polyprotein × 60 (A0A7D0TR32) Genome polyprotein × 60 (A0A4P2SK07) Genome polyprotein × 60 (E3VJS6) Kremen protein 1 × 60 (Q96MU8) STE STEARIC ACID × 60 MYR MYRISTIC ACID × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–305 Not recorded Genome polyprotein × 1 (A0A7D0TR32) Genome polyprotein × 1 (A0A4P2SK07) Genome polyprotein × 1 (E3VJS6) Kremen protein 1 × 1 (Q96MU8) STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain A; UniProt 1–305 Not recorded Genome polyprotein × 5 (A0A7D0TR32) Genome polyprotein × 5 (A0A4P2SK07) Genome polyprotein × 5 (E3VJS6) Kremen protein 1 × 5 (Q96MU8) STE STEARIC ACID × 5 MYR MYRISTIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain A; UniProt 1–305 Not recorded Genome polyprotein × 6 (A0A7D0TR32) Genome polyprotein × 6 (A0A4P2SK07) Genome polyprotein × 6 (E3VJS6) Kremen protein 1 × 6 (Q96MU8) STE STEARIC ACID × 6 MYR MYRISTIC ACID × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–305 Not recorded Genome polyprotein × 1 (A0A7D0TR32) Genome polyprotein × 1 (A0A4P2SK07) Genome polyprotein × 1 (E3VJS6) Kremen protein 1 × 1 (Q96MU8) STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A222NWY2_9ENTO
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–305; UniProt 1–305

Genome polyprotein

OrganismNot specified

UniProt A0A7D0TR32

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 300 PDB declaration: 300-meric(300) Consistent with protein copy count Chain B; UniProt 70–325 Not recorded Genome polyprotein × 60 (A0A222NWY2) Genome polyprotein × 60 (A0A4P2SK07) Genome polyprotein × 60 (E3VJS6) Kremen protein 1 × 60 (Q96MU8) STE STEARIC ACID × 60 MYR MYRISTIC ACID × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 70–325 Not recorded Genome polyprotein × 1 (A0A222NWY2) Genome polyprotein × 1 (A0A4P2SK07) Genome polyprotein × 1 (E3VJS6) Kremen protein 1 × 1 (Q96MU8) STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain B; UniProt 70–325 Not recorded Genome polyprotein × 5 (A0A222NWY2) Genome polyprotein × 5 (A0A4P2SK07) Genome polyprotein × 5 (E3VJS6) Kremen protein 1 × 5 (Q96MU8) STE STEARIC ACID × 5 MYR MYRISTIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain B; UniProt 70–325 Not recorded Genome polyprotein × 6 (A0A222NWY2) Genome polyprotein × 6 (A0A4P2SK07) Genome polyprotein × 6 (E3VJS6) Kremen protein 1 × 6 (Q96MU8) STE STEARIC ACID × 6 MYR MYRISTIC ACID × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 70–325 Not recorded Genome polyprotein × 1 (A0A222NWY2) Genome polyprotein × 1 (A0A4P2SK07) Genome polyprotein × 1 (E3VJS6) Kremen protein 1 × 1 (Q96MU8) STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A7D0TR32_9ENTO
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–256; UniProt 70–325

Genome polyprotein

OrganismNot specified

UniProt A0A4P2SK07

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 300 PDB declaration: 300-meric(300) Consistent with protein copy count Chain C; UniProt 326–565 Not recorded Genome polyprotein × 60 (A0A222NWY2) Genome polyprotein × 60 (A0A7D0TR32) Genome polyprotein × 60 (E3VJS6) Kremen protein 1 × 60 (Q96MU8) STE STEARIC ACID × 60 MYR MYRISTIC ACID × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 326–565 Not recorded Genome polyprotein × 1 (A0A222NWY2) Genome polyprotein × 1 (A0A7D0TR32) Genome polyprotein × 1 (E3VJS6) Kremen protein 1 × 1 (Q96MU8) STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain C; UniProt 326–565 Not recorded Genome polyprotein × 5 (A0A222NWY2) Genome polyprotein × 5 (A0A7D0TR32) Genome polyprotein × 5 (E3VJS6) Kremen protein 1 × 5 (Q96MU8) STE STEARIC ACID × 5 MYR MYRISTIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain C; UniProt 326–565 Not recorded Genome polyprotein × 6 (A0A222NWY2) Genome polyprotein × 6 (A0A7D0TR32) Genome polyprotein × 6 (E3VJS6) Kremen protein 1 × 6 (Q96MU8) STE STEARIC ACID × 6 MYR MYRISTIC ACID × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 326–565 Not recorded Genome polyprotein × 1 (A0A222NWY2) Genome polyprotein × 1 (A0A7D0TR32) Genome polyprotein × 1 (E3VJS6) Kremen protein 1 × 1 (Q96MU8) STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A4P2SK07_9ENTO
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–240; UniProt 326–565

Genome polyprotein

OrganismNot specified

UniProt E3VJS6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 300 PDB declaration: 300-meric(300) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded Genome polyprotein × 60 (A0A222NWY2) Genome polyprotein × 60 (A0A7D0TR32) Genome polyprotein × 60 (A0A4P2SK07) Kremen protein 1 × 60 (Q96MU8) STE STEARIC ACID × 60 MYR MYRISTIC ACID × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded Genome polyprotein × 1 (A0A222NWY2) Genome polyprotein × 1 (A0A7D0TR32) Genome polyprotein × 1 (A0A4P2SK07) Kremen protein 1 × 1 (Q96MU8) STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded Genome polyprotein × 5 (A0A222NWY2) Genome polyprotein × 5 (A0A7D0TR32) Genome polyprotein × 5 (A0A4P2SK07) Kremen protein 1 × 5 (Q96MU8) STE STEARIC ACID × 5 MYR MYRISTIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded Genome polyprotein × 6 (A0A222NWY2) Genome polyprotein × 6 (A0A7D0TR32) Genome polyprotein × 6 (A0A4P2SK07) Kremen protein 1 × 6 (Q96MU8) STE STEARIC ACID × 6 MYR MYRISTIC ACID × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded Genome polyprotein × 1 (A0A222NWY2) Genome polyprotein × 1 (A0A7D0TR32) Genome polyprotein × 1 (A0A4P2SK07) Kremen protein 1 × 1 (Q96MU8) STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name E3VJS6_9ENTO
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–69; UniProt 1–69

Kremen protein 1

Homo sapiens

UniProt Q96MU8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 300 PDB declaration: 300-meric(300) Consistent with protein copy count Chain G; UniProt 30–322 Not recorded Genome polyprotein × 60 (A0A222NWY2) Genome polyprotein × 60 (A0A7D0TR32) Genome polyprotein × 60 (A0A4P2SK07) Genome polyprotein × 60 (E3VJS6) STE STEARIC ACID × 60 MYR MYRISTIC ACID × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 30–322 Not recorded Genome polyprotein × 1 (A0A222NWY2) Genome polyprotein × 1 (A0A7D0TR32) Genome polyprotein × 1 (A0A4P2SK07) Genome polyprotein × 1 (E3VJS6) STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain G; UniProt 30–322 Not recorded Genome polyprotein × 5 (A0A222NWY2) Genome polyprotein × 5 (A0A7D0TR32) Genome polyprotein × 5 (A0A4P2SK07) Genome polyprotein × 5 (E3VJS6) STE STEARIC ACID × 5 MYR MYRISTIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain G; UniProt 30–322 Not recorded Genome polyprotein × 6 (A0A222NWY2) Genome polyprotein × 6 (A0A7D0TR32) Genome polyprotein × 6 (A0A4P2SK07) Genome polyprotein × 6 (E3VJS6) STE STEARIC ACID × 6 MYR MYRISTIC ACID × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 30–322 Not recorded Genome polyprotein × 1 (A0A222NWY2) Genome polyprotein × 1 (A0A7D0TR32) Genome polyprotein × 1 (A0A4P2SK07) Genome polyprotein × 1 (E3VJS6) STE STEARIC ACID × 1 MYR MYRISTIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.55 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KREM1_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain G; PDBConstruct 1–293; UniProt 30–322

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9vfr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9vfr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9vfr
Deposition date deposition_date2025-06-11
Structure title titleStructure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1
Keywords keywordscoxsackievirus A6, KRM1, receptor, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.70
Radius of gyration Rg (electron density) rg_electron33.17
Forward intensity I(0) i0223557000.00
Molecular weight molecular_weight120110.0 kDa
Excluded volume excluded_volume150030 ų
Envelope volume envelope_volume187850 ų
Hydration-shell volume shell_volume46785 ų
Envelope diameter envelope_diameter121.0
Shell Rg shell_rg40.14
Envelope Rg envelope_rg33.60
Shape Rg shape_rg33.17
Total Rg total_rg33.70
Total atoms total_atoms8479
Residues n_residues1119
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax114.2
Rg (real space) rg_real33.70
Rg uncertainty (real space) rg_real_error0.92
I(0) (real space) i0_real2.2360e+08
I(0) uncertainty (real space) i0_real_error3.7760e+06
Rg (reciprocal space) rg_reciprocal33.70
I(0) (reciprocal space) i0_reciprocal223600000.0000
Solution quality estimate total_estimate0.8794
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.9
Skewness Skewness skewness0.360
Kurtosis Kurtosis kurtosis-0.278
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28770000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.937

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)