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- PDB-1rvf: FAB COMPLEXED WITH INTACT HUMAN RHINOVIRUS -

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Basic information

Entry
Database: PDB / ID: 1rvf
TitleFAB COMPLEXED WITH INTACT HUMAN RHINOVIRUS
Components
  • (FAB 17-IA) x 2
  • (HUMAN RHINOVIRUS 14 COAT ...) x 4
KeywordsVirus/Immune system / POLYPROTEIN / COAT PROTEIN / CORE PROTEIN / RNA-DIRECTED RNA POLYMERASE / HYDROLASE / THIOL PROTEASE / MYRISTYLATION / COMPLEX (COAT PROTEIN-IMMUNOGLOBULIN) / Icosahedral virus / Virus-Immune system COMPLEX
Function / homology
Function and homology information


lysis of host organelle involved in viral entry into host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...lysis of host organelle involved in viral entry into host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / 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 / Immunoglobulin V-Type / Picornavirus/Calicivirus coat protein / Immunoglobulin V-set domain / Viral coat protein subunit / Immunoglobulin V-set domain / Few Secondary Structures / Irregular / Immunoglobulin subtype / Immunoglobulin / 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. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
: / : / Genome polyprotein / Anti-VIPase light chain variable region
Similarity search - Component
Biological speciesHuman rhinovirus 14
Human rhinovirus sp.
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsSmith, T.J.
Citation
Journal: Nature / Year: 1996
Title: Neutralizing antibody to human rhinovirus 14 penetrates the receptor-binding canyon.
Authors: Smith, T.J. / Chase, E.S. / Schmidt, T.J. / Olson, N.H. / Baker, T.S.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Structure Determination of an Fab Fragment that Neutralizes Human Rhinovirus 14 and Analysis of the Fab-Virus Complex
Authors: Liu, H. / Smith, T.J. / Lee, W.M. / Mosser, A.G. / Rueckert, R.R. / Olson, N.H. / Cheng, R.H. / Baker, T.S.
#2: Journal: Nature / Year: 1985
Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G.
History
DepositionSep 5, 1996Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _pdbx_validate_close_contact.dist / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref_seq_dif.details
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: HUMAN RHINOVIRUS 14 COAT PROTEIN
2: HUMAN RHINOVIRUS 14 COAT PROTEIN
3: HUMAN RHINOVIRUS 14 COAT PROTEIN
4: HUMAN RHINOVIRUS 14 COAT PROTEIN
L: FAB 17-IA
H: FAB 17-IA


Theoretical massNumber of molelcules
Total (without water)119,3736
Polymers119,3736
Non-polymers00
Water0
1
1: HUMAN RHINOVIRUS 14 COAT PROTEIN
2: HUMAN RHINOVIRUS 14 COAT PROTEIN
3: HUMAN RHINOVIRUS 14 COAT PROTEIN
4: HUMAN RHINOVIRUS 14 COAT PROTEIN
L: FAB 17-IA
H: FAB 17-IA
x 60


Theoretical massNumber of molelcules
Total (without water)7,162,390360
Polymers7,162,390360
Non-polymers00
Water0
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: HUMAN RHINOVIRUS 14 COAT PROTEIN
2: HUMAN RHINOVIRUS 14 COAT PROTEIN
3: HUMAN RHINOVIRUS 14 COAT PROTEIN
4: HUMAN RHINOVIRUS 14 COAT PROTEIN
L: FAB 17-IA
H: FAB 17-IA
x 5


  • icosahedral pentamer
  • 597 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)596,86630
Polymers596,86630
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: HUMAN RHINOVIRUS 14 COAT PROTEIN
2: HUMAN RHINOVIRUS 14 COAT PROTEIN
3: HUMAN RHINOVIRUS 14 COAT PROTEIN
4: HUMAN RHINOVIRUS 14 COAT PROTEIN
L: FAB 17-IA
H: FAB 17-IA
x 6


  • icosahedral 23 hexamer
  • 716 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)716,23936
Polymers716,23936
Non-polymers00
Water0
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: HUMAN RHINOVIRUS 14 COAT PROTEIN
2: HUMAN RHINOVIRUS 14 COAT PROTEIN
3: HUMAN RHINOVIRUS 14 COAT PROTEIN
4: HUMAN RHINOVIRUS 14 COAT PROTEIN
L: FAB 17-IA
H: FAB 17-IA
x 20


  • crystal asymmetric unit, crystal frame
  • 120-MERIC
  • 2.39 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,387,463120
Polymers2,387,463120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation19
Unit cell
Length a, b, c (Å)372.000, 372.000, 372.000
Angle α, β, γ (deg.)108.40, 108.40, 108.40
Int Tables number146
Space group name H-MR3
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.31272137, -0.94988818, -0.00589133), (0.94516943, 0.31043215, 0.10090488), (-0.09395152, -0.03706633, 0.99488046)
3generate(-0.79945712, -0.5917078, -0.10355186), (0.5795055, -0.80517733, 0.12614411), (-0.15788514, 0.04086029, 0.98660046)
4generate(-0.7995426, 0.57954803, -0.15801806), (-0.59165668, -0.80509405, 0.04083793), (-0.10344678, 0.12608792, 0.98660267)
5generate(0.31258306, 0.94524355, -0.0940195), (-0.94981077, 0.31056689, -0.03712341), (-0.00586839, 0.10083488, 0.99488404)
6generate(-0.65520948, 0.29039074, -0.69752249), (0.2903304, -0.75547685, -0.58734792), (-0.69731267, -0.58729323, 0.41068634)
7generate(0.13510374, 0.73837696, -0.66078961), (-0.56807888, -0.48853489, -0.6622827), (-0.81174081, 0.46483172, 0.35343116)
8generate(0.80222336, 0.12537555, -0.58369677), (-0.57717618, 0.41250286, -0.70484093), (0.15229064, 0.90226131, 0.40330777)
9generate(0.42421273, -0.70146638, -0.57278367), (0.27561064, 0.70243285, -0.65620858), (0.86252297, 0.12048271, 0.49138839)
10generate(-0.4765303, -0.59948138, -0.64313183), (0.81175921, -0.01941831, -0.58359391), (0.33743925, -0.80011263, 0.4959486)
11generate(-0.43000582, 0.69814951, 0.57251595), (0.69811936, -0.14491811, 0.70120799), (0.57239156, 0.7010859, -0.42507607)
12generate(0.47160883, 0.60396443, 0.64256492), (0.01546513, -0.73411378, 0.67888234), (0.88158059, -0.31031236, -0.35552903)
13generate(0.65796094, -0.2843032, 0.69743985), (-0.75280767, -0.26774634, 0.60124), (0.01579384, -0.92055576, -0.3902146)
14generate(-0.12848178, -0.73909771, 0.66130543), (-0.54497212, 0.60968027, 0.57558005), (-0.82848084, -0.28630866, -0.48119849)
15generate(-0.80088221, -0.13190853, 0.58409822), (0.3517501, 0.68559229, 0.63736367), (-0.48448453, 0.715921, -0.50274406)
16generate(0.0852153, -0.98854025, 0.12500655), (-0.98844977, -0.09960504, -0.11386008), (0.12492111, -0.11379267, -0.98561027)
17generate(-0.91943394, -0.39245322, 0.02411601), (-0.39255568, 0.91221652, -0.11750451), (0.02411174, -0.11745303, -0.99278259)
18generate(-0.66072718, 0.75063544, -0.01019122), (0.75047836, 0.6604208, -0.02254318), (-0.01019933, -0.02256584, -0.99969363)
19generate(0.50381165, 0.86101606, 0.0694963), (0.86101815, -0.50701908, 0.0397906), (0.06940465, 0.03973803, -0.99679258)
20generate(0.96482945, -0.21385363, 0.15305311), (-0.21369854, -0.97674088, -0.01664634), (0.15291367, -0.01664325, -0.98808858)

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Components

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HUMAN RHINOVIRUS 14 COAT ... , 4 types, 4 molecules 1234

#1: Protein HUMAN RHINOVIRUS 14 COAT PROTEIN


Mass: 32560.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Strain: SEROTYPE 14 / References: UniProt: P03303
#2: Protein HUMAN RHINOVIRUS 14 COAT PROTEIN


Mass: 28501.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Strain: SEROTYPE 14 / References: UniProt: P03303
#3: Protein HUMAN RHINOVIRUS 14 COAT PROTEIN


Mass: 26236.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Strain: SEROTYPE 14 / References: UniProt: P03303
#4: Protein HUMAN RHINOVIRUS 14 COAT PROTEIN


Mass: 7183.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 14 / References: UniProt: P03303

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Antibody , 2 types, 2 molecules LH

#5: Antibody FAB 17-IA


Mass: 11884.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: EMBL: X79906, UniProt: Q8K1F2*PLUS
#6: Antibody FAB 17-IA


Mass: 13006.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: PIR: S38950

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Experimental details

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Experiment

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

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Sample preparation

Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
2250-300 mM1dropNaCl
310 mM1dropCaCl2
40.75 %PEG80001drop
510 mMTris-HCl1reservoir
610 mM1reservoirCaCl2
70.75 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 3, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionNum. obs: 259123 / % possible obs: 64.5 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Rmerge(I) obs: 0.166
Reflection shellResolution: 4→4.18 Å / Redundancy: 1.5 % / Rsym value: 0.293 / % possible all: 46.9
Reflection
*PLUS
Highest resolution: 4 Å / Lowest resolution: 20 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
ENVELOPEmodel building
X-PLOR3.1refinement
ENVELOPEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEE REFERENCE 1

Resolution: 4→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.212 --
obs0.212 259123 64.5 %
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 0 0 8020
Refine LS restraints NCSNCS model details: ICOSAHEDRAL 20-FOLD
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2

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