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- PDB-1qqp: FOOT-AND-MOUTH DISEASE VIRUS/ OLIGOSACCHARIDE RECEPTOR COMPLEX. -

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Basic information

Entry
Database: PDB / ID: 1qqp
TitleFOOT-AND-MOUTH DISEASE VIRUS/ OLIGOSACCHARIDE RECEPTOR COMPLEX.
Components(PROTEIN (GENOME ...) x 4
KeywordsVIRUS / HEPARAN SULPHATE / VIRUS-RECEPTOR INTERACTIONS/PROTEIN-CARBOHYDRATE INTERACTIONS / VIRUS/VIRAL PROTEIN / Icosahedral virus
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / regulation of translation / channel activity / monoatomic ion transmembrane transport ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / molecular adaptor activity / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type ...Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / Papain-like cysteine peptidase superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Few Secondary Structures / Irregular / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesFoot-and-mouth disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsFry, E.E. / Lea, S.M. / Jackson, T. / Newman, J.W.I. / Ellard, F.M. / Blakemore, W.E. / Abu-Ghazaleh, R. / Samuel, A. / King, A.M.Q. / Stuart, D.I.
Citation
Journal: EMBO J. / Year: 1999
Title: The structure and function of a foot-and-mouth disease virus-oligosaccharide receptor complex.
Authors: Fry, E.E. / Lea, S.M. / Jackson, T. / Newman, J.W. / Ellard, F.M. / Blakemore, W.E. / Abu-Ghazaleh, R. / Samuel, A. / King, A.M. / Stuart, D.I.
#1: Journal: Nature / Year: 1993
Title: Structure of a Major Immunogenic Site on Foot-and-Mouth Disease Virus
Authors: Logan, D. / Abu-Ghazaleh, R. / Blakemore, W. / Curry, S. / Jackson, T. / King, A. / Lea, S. / Lewis, R. / Stuart, D. / Fry, E.
#2: Journal: Nature / Year: 1989
Title: The Three-Dimensional Structure of Foot-and-Mouth Disease Virus at 2.9 Angstroms Resolution
Authors: Acharya, R. / Fry, E. / Stuart, D. / Fox, G. / Rowlands, D. / Brown, F.
History
DepositionMay 20, 1999Deposition site: RCSB / Processing site: RCSB
SupersessionJun 18, 1999ID: 1FHP
Revision 1.0Jun 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: PROTEIN (GENOME POLYPROTEIN)
2: PROTEIN (GENOME POLYPROTEIN)
3: PROTEIN (GENOME POLYPROTEIN)
4: PROTEIN (GENOME POLYPROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2705
Polymers80,8414
Non-polymers1,4291
Water11,367631
1
1: PROTEIN (GENOME POLYPROTEIN)
2: PROTEIN (GENOME POLYPROTEIN)
3: PROTEIN (GENOME POLYPROTEIN)
4: PROTEIN (GENOME POLYPROTEIN)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,936,185300
Polymers4,850,436240
Non-polymers85,74960
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: PROTEIN (GENOME POLYPROTEIN)
2: PROTEIN (GENOME POLYPROTEIN)
3: PROTEIN (GENOME POLYPROTEIN)
4: PROTEIN (GENOME POLYPROTEIN)
hetero molecules
x 5


  • icosahedral pentamer
  • 411 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)411,34925
Polymers404,20320
Non-polymers7,1465
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: PROTEIN (GENOME POLYPROTEIN)
2: PROTEIN (GENOME POLYPROTEIN)
3: PROTEIN (GENOME POLYPROTEIN)
4: PROTEIN (GENOME POLYPROTEIN)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 494 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)493,61830
Polymers485,04424
Non-polymers8,5756
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
1: PROTEIN (GENOME POLYPROTEIN)
2: PROTEIN (GENOME POLYPROTEIN)
3: PROTEIN (GENOME POLYPROTEIN)
4: PROTEIN (GENOME POLYPROTEIN)
hetero molecules
x 5


  • crystal asymmetric unit, crystal frame
  • 411 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)411,34925
Polymers404,20320
Non-polymers7,1465
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)345.000, 345.000, 345.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.80901699, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699)
3generate(-0.30901699, -0.5, 0.80901699), (0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5)
4generate(-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5)
5generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)

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Components

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PROTEIN (GENOME ... , 4 types, 4 molecules 1234

#1: Protein PROTEIN (GENOME POLYPROTEIN) / FMDV


Mass: 23828.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN BHK CELLS / Source: (natural) Foot-and-mouth disease virus / Genus: Aphthovirus / References: UniProt: P03305
#2: Protein PROTEIN (GENOME POLYPROTEIN) / FMDV


Mass: 24373.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN BHK CELLS / Source: (natural) Foot-and-mouth disease virus / Genus: Aphthovirus / References: UniProt: P03305
#3: Protein PROTEIN (GENOME POLYPROTEIN) / FMDV


Mass: 23860.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN BHK CELLS / Source: (natural) Foot-and-mouth disease virus / Genus: Aphthovirus / References: UniProt: P03305
#4: Protein PROTEIN (GENOME POLYPROTEIN) / FMDV


Mass: 8778.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN BHK CELLS / Source: (natural) Foot-and-mouth disease virus / Genus: Aphthovirus / References: UniProt: P03305

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Sugars / Non-polymers , 2 types, 632 molecules

#5: Polysaccharide 2-O-sulfo-alpha-L-gulopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-gulopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 1429.144 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,5,4/[a1121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-3-2-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-GulpA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-AllpA2SO3]{}}}}}LINUCSPDB-CARE
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
pH: 7.6 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
20.1 Msodium phosphate11
1ammonium sulfate11

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→12 Å / Num. obs: 2070213 / % possible obs: 91 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.143
Reflection shell
*PLUS
% possible obs: 77.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1refinement
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1BTT

1btt


Resolution: 1.9→12 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0
Details: THE DENSITY WAS TOO WEAK TO MODEL THE SIDE CHAINS ACCURATELY FOR CHAIN 1 RESIDUES ARG 157 AND THR 158.
RfactorNum. reflection% reflection
Rwork0.161 --
obs0.161 480760 91 %
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5201 0 85 631 5917
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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