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- PDB-1zba: Foot-and-Mouth Disease virus serotype A1061 complexed with oligos... -

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Basic information

Entry
Database: PDB / ID: 1zba
TitleFoot-and-Mouth Disease virus serotype A1061 complexed with oligosaccharide receptor.
Components(Coat protein ...) x 4
KeywordsVIRUS / oligosaccharide receptor / VIRUS/VIRAL PROTEIN / Icosahedral virus
Function / homology
Function and homology information


: / L-peptidase / modulation by virus of host chromatin organization / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...: / L-peptidase / modulation by virus of host chromatin organization / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 / Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Papain-like cysteine peptidase superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures / Irregular / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFry, E.E. / Newman, J.W. / Curry, S. / Najjam, S. / Jackson, T. / Blakemore, W. / Lea, S.M. / Miller, L. / Burman, A. / King, A.M. / Stuart, D.I.
CitationJournal: J.Gen.Virol. / Year: 2005
Title: Structure of Foot-and-mouth disease virus serotype A1061 alone and complexed with oligosaccharide receptor: receptor conservation in the face of antigenic variation.
Authors: Fry, E.E. / Newman, J.W. / Curry, S. / Najjam, S. / Jackson, T. / Blakemore, W. / Lea, S.M. / Miller, L. / Burman, A. / King, A.M. / Stuart, D.I.
History
DepositionApr 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / 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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 14, 2024Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Coat protein VP1
2: Coat protein VP2
3: Coat protein VP3
4: Coat protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9175
Polymers81,0004
Non-polymers9171
Water8,107450
1
1: Coat protein VP1
2: Coat protein VP2
3: Coat protein VP3
4: Coat protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,915,030300
Polymers4,860,023240
Non-polymers55,00660
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: Coat protein VP1
2: Coat protein VP2
3: Coat protein VP3
4: Coat protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 410 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)409,58625
Polymers405,00220
Non-polymers4,5845
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Coat protein VP1
2: Coat protein VP2
3: Coat protein VP3
4: Coat protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 492 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)491,50330
Polymers486,00224
Non-polymers5,5016
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: Coat protein VP1
2: Coat protein VP2
3: Coat protein VP3
4: Coat protein VP4
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.64 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,638,343100
Polymers1,620,00880
Non-polymers18,33520
Water1,44180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)307.000, 307.000, 715.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.49658956, -0.64359727, 0.5823928), (0.86792531, 0.37608847, -0.32444278), (-0.01022073, 0.66658835, 0.74535596)
3generate(-0.31794565, -0.17343694, 0.93211061), (0.76073539, -0.6334216, 0.1416289), (0.56585531, 0.75411982, 0.33333326)
4generate(-0.31794565, 0.76073539, 0.56585531), (-0.17343694, -0.6334216, 0.75411982), (0.93211061, 0.1416289, 0.33333326)
5generate(0.49658956, 0.86792531, -0.01022073), (-0.64359727, 0.37608847, 0.66658835), (0.5823928, -0.32444278, 0.74535596)
6generate(-0.52631596, 0.85028907, -5.0E-8), (0.85028907, 0.52631596, -1.0E-7), (-5.0E-8, -1.0E-7, -1)
7generate(0.4766244, 0.65851939, -0.58239282), (0.87904762, -0.34930243, 0.32444275), (0.01022062, -0.66658835, -0.74535596)
8generate(0.81418483, -0.44730888, -0.3701592), (0.13004141, -0.48085151, 0.86710499), (-0.56585537, -0.75411975, -0.33333332)
9generate(0.01986828, -0.93897865, 0.34340114), (-0.36162843, 0.31346508, 0.87804586), (-0.93211058, -0.14162888, -0.33333336)
10generate(-0.80860677, -0.13701901, 0.57217208), (0.08350911, 0.9359288, 0.34214544), (-0.58239276, 0.3244427, -0.74535603)
11generate(0.80324525, -0.09065444, 0.58870947), (0.48669578, -0.46991189, -0.73641702), (0.34340105, 0.87804589, -0.33333336)
12generate(0.31418488, -0.15863366, 0.93601454), (-0.15863366, -0.98085152, -0.11298518), (0.93601454, -0.11298518, -0.33333336)
13generate(0.00877201, 0.36206757, 0.93211058), (-0.92892689, -0.34210536, 0.14162892), (0.37015926, -0.86710495, 0.33333335)
14generate(0.30907685, 0.75185784, 0.58239273), (-0.75966485, 0.56360111, -0.32444276), (-0.57217202, -0.34214554, 0.74535603)
15generate(0.80008831, 0.47206026, 0.37015917), (0.11523808, 0.48461233, -0.86710499), (-0.5887095, 0.736417, 0.33333334)
16generate(-0.00892871, -0.35184811, -0.93601452), (0.93914638, -0.32440469, 0.11298523), (-0.34340114, -0.87804584, 0.3333334)
17generate(-0.30024504, -0.7505159, -0.58870944), (0.18365645, -0.65112227, 0.73641707), (-0.93601454, 0.11298528, 0.33333332)
18generate(-0.79447326, -0.48145034, -0.37015917), (-0.48145034, 0.12780667, 0.86710497), (-0.37015917, 0.86710497, -0.33333341)
19generate(-0.80860677, 0.08350911, -0.58239276), (-0.13701901, 0.9359288, 0.3244427), (0.57217208, 0.34214544, -0.74535603)
20generate(-0.32311353, 0.16360769, -0.9321106), (0.74095805, 0.65644681, -0.14162893), (0.58870945, -0.73641707, -0.33333328)

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Components

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Coat protein ... , 4 types, 4 molecules 1234

#1: Protein Coat protein VP1


Mass: 23293.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus / Genus: Aphthovirus / References: UniProt: Q84769, UniProt: P03306*PLUS
#2: Protein Coat protein VP2


Mass: 24678.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus / Genus: Aphthovirus / References: UniProt: Q84769, UniProt: P03306*PLUS
#3: Protein Coat protein VP3


Mass: 24233.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus / Genus: Aphthovirus / References: UniProt: Q84769, UniProt: P03306*PLUS
#4: Protein Coat protein VP4


Mass: 8794.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus / Genus: Aphthovirus / References: UniProt: Q84769, UniProt: P03306*PLUS

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Sugars / Non-polymers , 2 types, 451 molecules

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


Type: oligosaccharide / Mass: 916.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[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]/1-2-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{}}}LINUCSPDB-CARE
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 452651 / Rmerge(I) obs: 0.135

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Processing

SoftwareName: X-PLOR / Version: 3.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
all0.183 --
obs0.183 452651 -
Rfree--Not valid for virus refinement
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5227 0 55 450 5732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.7

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