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1d4m

THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS A9 TO 2.9 A RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 93.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (COXSACKIEVIRUS A9)

OrganismNot specified

UniProt P21404

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 homooligomer Homooligomer Protein × 240 PDB declaration: 240-MERIC（240） Consistent with protein copy count Chain 1； UniProt 568–866 Chain 2； UniProt 69–329 Chain 3； UniProt 330–567 Chain 4； UniProt 1–68 Fragment：VP1 Fragment：VP2 Fragment：VP3 Fragment：VP4 W71 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 120 MYR MYRISTIC ACID × 60 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 Å
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain 1； UniProt 568–866 Chain 2； UniProt 69–329 Chain 3； UniProt 330–567 Chain 4； UniProt 1–68 Fragment：VP1 Fragment：VP2 Fragment：VP3 Fragment：VP4 W71 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 2 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 Å
3 Protein homooligomer Homooligomer Protein × 20 PDB declaration: eicosameric（20） Consistent with protein copy count Chain 1； UniProt 568–866 Chain 2； UniProt 69–329 Chain 3； UniProt 330–567 Chain 4； UniProt 1–68 Fragment：VP1 Fragment：VP2 Fragment：VP3 Fragment：VP4 W71 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 10 MYR MYRISTIC ACID × 5 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 Å
4 Protein homooligomer Homooligomer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain 1； UniProt 568–866 Chain 2； UniProt 69–329 Chain 3； UniProt 330–567 Chain 4； UniProt 1–68 Fragment：VP1 Fragment：VP2 Fragment：VP3 Fragment：VP4 W71 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 12 MYR MYRISTIC ACID × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 Å
5 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain 1； UniProt 568–866 Chain 2； UniProt 69–329 Chain 3； UniProt 330–567 Chain 4； UniProt 1–68 Fragment：VP1 Fragment：VP2 Fragment：VP3 Fragment：VP4 W71 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 2 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 Å
6 Protein homooligomer Homooligomer Protein × 120 PDB declaration: 120-meric（120） Consistent with protein copy count Chain 1； UniProt 568–866 Chain 2； UniProt 69–329 Chain 3； UniProt 330–567 Chain 4； UniProt 1–68 Fragment：VP1 Fragment：VP2 Fragment：VP3 Fragment：VP4 W71 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 60 MYR MYRISTIC ACID × 30 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 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.

Other PDB Difference from Current Entry 1D4M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J2J Empty coxsackievirus A9 capsid Deposited 2012-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric
Chain A 631–852（222 aa） Fragment：UNP residues 631-852
Chain B 331–568（238 aa） Fragment：UNP residues 331-568
Chain C 79–330（252 aa） Fragment：UNP residues 79-330
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions manual plunging；Cryogen ETHANE；manual plunging into liquid ethane (GATAN CRYOPLUNGE 3)
Resolution 9.54 Å
3J2J Empty coxsackievirus A9 capsid Deposited 2012-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 631–852（222 aa） Fragment：UNP residues 631-852
Chain B 331–568（238 aa） Fragment：UNP residues 331-568
Chain C 79–330（252 aa） Fragment：UNP residues 79-330
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions manual plunging；Cryogen ETHANE；manual plunging into liquid ethane (GATAN CRYOPLUNGE 3)
Resolution 9.54 Å
3J2J Empty coxsackievirus A9 capsid Deposited 2012-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 631–852（222 aa） Fragment：UNP residues 631-852
Chain B 331–568（238 aa） Fragment：UNP residues 331-568
Chain C 79–330（252 aa） Fragment：UNP residues 79-330
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions manual plunging；Cryogen ETHANE；manual plunging into liquid ethane (GATAN CRYOPLUNGE 3)
Resolution 9.54 Å
3J2J Empty coxsackievirus A9 capsid Deposited 2012-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain A 631–852（222 aa） Fragment：UNP residues 631-852
Chain B 331–568（238 aa） Fragment：UNP residues 331-568
Chain C 79–330（252 aa） Fragment：UNP residues 79-330
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions manual plunging；Cryogen ETHANE；manual plunging into liquid ethane (GATAN CRYOPLUNGE 3)
Resolution 9.54 Å
3J2J Empty coxsackievirus A9 capsid Deposited 2012-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 631–852（222 aa） Fragment：UNP residues 631-852
Chain B 331–568（238 aa） Fragment：UNP residues 331-568
Chain C 79–330（252 aa） Fragment：UNP residues 79-330
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions manual plunging；Cryogen ETHANE；manual plunging into liquid ethane (GATAN CRYOPLUNGE 3)
Resolution 9.54 Å
8AT5 native Coxsackievirus A9 Deposited 2022-08-22 Different construct Different ligand/ion Different experimental method Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 569–867（299 aa）
Chain B 70–330（261 aa）
Chain C 331–568（238 aa）
Chain D 2–69（68 aa）
Not recorded MYR MYRISTIC ACID × 60 PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.25；PBS containing 2mM MgCl2, pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8AW6 Expanded Coxsackievirus A9 after 0.01% faf-BSA treatment Deposited 2022-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric
Chain A 569–867（299 aa）
Chain B 70–330（261 aa）
Chain C 331–568（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.25；DPBS containing 0.01% faf-BSA, pH 7.25, incubated at 37 C for 1 h
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8AXX Expanded Coxsackievirus A9 after treatment with endosomal ionic buffer Deposited 2022-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric
Chain A 569–867（299 aa）
Chain B 70–330（261 aa）
Chain C 331–568（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.25；endosomal ionic composition buffer, pH 7.25, incubated at 37 C for 3 h 20 mM NaCl, 6 mM KH2PO4, 12 mM K2HPO4, 0.5 mM MgCl2, 0.45 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8S7J Coxsackievirus A9 bound with compound 20 (CL300) Deposited 2024-03-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 569–867（299 aa）
Chain B 70–330（261 aa）
Chain C 331–568（238 aa）
Chain D 2–69（68 aa）
Not recorded A1H9Q ~{N}-[(4-methoxyphenyl)methyl]-4-[(4-methylpiperazin-1-yl)methyl]aniline × 60 MYR MYRISTIC ACID × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；PBS containing 2 mM MgCl2 and 5% DMSO.
cryo-EM vitrification conditions Cryogen ETHANE；Sample was incubated for 15 s on the grid before blotted from the front for 1.5 s.
Resolution 2.26 Å
9EXI Coxsackievirus A9 bound with compound 14 (CL275) Deposited 2024-04-08 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 569–851（283 aa）
Chain B 79–329（251 aa）
Chain C 331–568（238 aa）
Chain D 2–69（68 aa）
Not recorded A1H8J 4-[(4-methylpiperazin-1-yl)methyl]-N-[[4-(trifluoromethyl)phenyl]methyl]aniline × 60 MYR MYRISTIC ACID × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；PBS containing 2 mM MgCl2 and 5% DMSO.
cryo-EM vitrification conditions Cryogen ETHANE；Sample was incubated for 15 s on the grid before blotted from the front for 1.5 s.
Resolution 2.31 Å
9FA9 Coxsackievirus A9 bound with compound 16 (CL298) Deposited 2024-05-10 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 569–851（283 aa）
Chain B 70–330（261 aa）
Chain C 331–568（238 aa）
Chain D 2–69（68 aa）
Not recorded A1IBS ~{N}-[(2-fluorophenyl)methyl]-4-[(4-methylpiperazin-1-yl)methyl]aniline × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；Sample was incubated for 15 s on the grid before blotted from the front for 1.5 s.
Resolution 2.75 Å
9FCZ Coxsackievirus A9 bound with compound 17 (CL301) Deposited 2024-05-16 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 569–851（283 aa）
Chain B 79–329（251 aa）
Chain C 331–568（238 aa）
Chain D 2–69（68 aa）
Not recorded A1IB2 ~{N}-[(3-fluorophenyl)methyl]-4-[(4-methylpiperazin-1-yl)methyl]aniline × 60 MYR MYRISTIC ACID × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；PBS containing 2 mM MgCl2 and 5% DMSO.
cryo-EM vitrification conditions Cryogen ETHANE；Sample was incubated for 15 s on the grid before blotted from the front for 1.5 s.
Resolution 2.53 Å
9FGN Coxsackievirus A9 bound with compound 18 (CL304) Deposited 2024-05-24 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 569–850（282 aa）
Chain B 79–328（250 aa）
Chain C 332–567（236 aa）
Chain D 2–68（67 aa）
Not recorded A1ICH ~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-4-[(4-methylpiperazin-1-yl)methyl]aniline × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；PBS containing 2 mM MgCl2 and 5% DMSO.
cryo-EM vitrification conditions Cryogen ETHANE；Sample was incubated for 15 s on the grid before blotted from the front for 1.5 s.
Resolution 2.64 Å
9FO2 Coxsackievirus A9 bound with compound 15 (CL278) Deposited 2024-06-11 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 569–867（299 aa）
Chain B 79–329（251 aa）
Chain C 331–568（238 aa）
Chain D 2–69（68 aa）
Not recorded A1IEI ~{N}-[(4-fluorophenyl)methyl]-4-[(4-methylpiperazin-1-yl)methyl]aniline × 60 MYR MYRISTIC ACID × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；Sample was blotted from the front for 1.5 s.
Resolution 2.58 Å
9FO5 Coxsackievirus A9 bound with compound 19 (CL313) Deposited 2024-06-11 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 569–867（299 aa）
Chain B 70–330（261 aa）
Chain C 331–568（238 aa）
Chain D 2–69（68 aa）
Not recorded A1IEH ~{N}-[[3,4-bis(fluoranyl)phenyl]methyl]-4-[(4-methylpiperazin-1-yl)methyl]aniline × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；Sample was incubated for 15 s on the grid before blotted from the front for 1.5 s.
Resolution 2.69 Å
9FP5 Coxsackievirus A9 bound with CL213. Deposited 2024-06-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 569–867（299 aa）
Chain B 70–330（261 aa）
Chain C 331–568（238 aa）
Chain D 2–69（68 aa）
Not recorded PLM PALMITIC ACID × 60 MYR MYRISTIC ACID × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；Sample was incubated for 15 s on the grid before blotted from the front for 1.5 s.
Resolution 2.50 Å

12 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_CXA9
Isoform —
PDB entities 1, 2, 3, 4
Chains and sequence ranges Author chain 1； PDBConstruct 1–299； UniProt 568–866 Author chain 2； PDBConstruct 1–261； UniProt 69–329 Author chain 3； PDBConstruct 1–238； UniProt 330–567 Author chain 4； PDBConstruct 1–68； UniProt 1–68

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 1d4m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d4m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d4m
Deposition date deposition_date1999-10-04
Structure title titleTHE CRYSTAL STRUCTURE OF COXSACKIEVIRUS A9 TO 2.9 A RESOLUTION
Keywords keywordsPICORNAVIRUS STRUCTURE, RGD, UNCOATING, VIRUS-RECEPTOR INTERACTION, WIN COMPOUND, VIRUS/VIRAL PROTEIN, Icosahedral virus, Virus; VIRUS
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.79 Å
Radius of gyration Rg (electron density) rg_electron28.86 Å
Forward intensity I(0) i0143043000.00
Molecular weight molecular_weight93946.0 kDa
Excluded volume excluded_volume117110 ų
Envelope volume envelope_volume146160 ų
Hydration-shell volume shell_volume41014 ų
Envelope diameter envelope_diameter101.6 Å
Shell Rg shell_rg37.10 Å
Envelope Rg envelope_rg29.54 Å
Shape Rg shape_rg28.85 Å
Total Rg total_rg29.65 Å
Total atoms total_atoms6603
Residues n_residues835
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax93.8 Å
Rg (real space) rg_real29.72 Å
Rg uncertainty (real space) rg_real_error0.53 Å
I(0) (real space) i0_real1.4300e+08
I(0) uncertainty (real space) i0_real_error2.1830e+06
Rg (reciprocal space) rg_reciprocal29.75 Å
I(0) (reciprocal space) i0_reciprocal143000000.0000
Solution quality estimate total_estimate0.8955
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.4 Å
Skewness Skewness skewness0.292
Kurtosis Kurtosis kurtosis-0.341
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27760000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.890
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1d4m.1
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
Domain ID domain_idd1d4m1_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
Domain ID domain_idd1d4m3_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

CATH v4.4 (4 domains)

Domain ID domain_id1d4m100
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1d4m200
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1d4m300
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1d4m400
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily10 — Picornavirus coat protein VP4
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8. Citations (2)

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9. Files and Curves (10)