[English] 日本語
Yorodumi
- PDB-4gbt: Structural characterization of H-1 Parvovirus: comparison of infe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gbt
TitleStructural characterization of H-1 Parvovirus: comparison of infectious virions to replication defective particles
ComponentsCapsid protein VP1
KeywordsVIRUS / Beta-barrel / icosahedral virus / Capsid / Capsid Proteins / Parvovirus / capsid protein
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesH-1 parvovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsHalder, S. / Nam, H.-J. / Govindasamy, L. / Vogel, M. / Dinsart, C. / Salome, N. / McKenna, R. / Agbandje-McKenna, M.
CitationJournal: J.Virol. / Year: 2013
Title: Structural characterization of h-1 parvovirus: comparison of infectious virions to empty capsids.
Authors: Halder, S. / Nam, H.J. / Govindasamy, L. / Vogel, M. / Dinsart, C. / Salome, N. / McKenna, R. / Agbandje-McKenna, M.
History
DepositionJul 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4003
Polymers81,3411
Non-polymers582
Water32418
1
A: Capsid protein VP1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,883,980180
Polymers4,880,47460
Non-polymers3,507120
Water1,08160
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
A: Capsid protein VP1
hetero molecules
x 5


  • icosahedral pentamer
  • 407 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)406,99815
Polymers406,7065
Non-polymers29210
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 488 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)488,39818
Polymers488,0476
Non-polymers35112
Water1086
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
A: Capsid protein VP1
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 4.88 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)4,883,980180
Polymers4,880,47460
Non-polymers3,507120
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)255.200, 350.100, 272.100
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1generate(1), (1), (1)
2generate(-0.52755, 0.30578, 0.79258), (-0.71935, -0.6571, -0.22529), (0.45192, -0.689, 0.56662)43.75523, 61.27755, 0.57187
3generate(0.31668, -0.26226, 0.91155), (-0.94787, -0.05171, 0.31442), (-0.03532, -0.96361, -0.26497)-18.27773, 39.20522, 88.21573
4generate(0.36806, -0.92088, 0.12851), (-0.37153, -0.01895, 0.92823), (-0.85235, -0.38939, -0.34911)31.64978, -39.33512, 146.14355
5generate(-0.44443, -0.75988, -0.4744), (0.2132, -0.60409, 0.76787), (-0.87007, 0.24012, 0.43049)124.53958, -65.80287, 94.2997
6generate(-0.56297, -0.59766, 0.57085), (-0.6416, 0.75143, 0.15396), (-0.52097, -0.27958, -0.80649)61.08585, 30.53726, 156.04778
7generate(-0.59747, -0.64265, 0.47961), (-0.64265, 0.02601, -0.76572), (0.47962, -0.76572, -0.42853)69.49085, 93.09936, 66.42532
8generate(-0.99881, 0.02965, 0.03873), (0.02965, -0.26141, 0.96477), (0.03873, 0.96477, 0.26022)125.09649, -67.45426, 47.79525
9generate(-0.53796, -0.71496, -0.44659), (-0.71496, 0.10631, 0.69104), (-0.44659, 0.69104, -0.56835)128.62577, -1.2712, 135.11243
10generate(0.28673, -0.95563, 0.06754), (-0.95563, -0.29027, -0.05017), (0.06755, -0.05016, -0.99645)40.99056, 64.47559, 131.34926
11generate(-0.44984, 0.89299, -0.01458), (-0.72176, -0.35387, 0.59484), (0.52603, 0.27811, 0.80371)93.63848, 5.70026, -20.27584
12generate(-0.44443, 0.21321, -0.87007), (-0.75988, -0.60409, 0.24012), (-0.47441, 0.76787, 0.43049)151.42616, 32.24161, 69.01506
13generate(-0.41164, 0.90414, -0.11436), (-0.71429, -0.39802, -0.57564), (-0.56598, -0.15527, 0.80966)97.97781, 84.76153, 49.10145
14generate(-0.34578, 0.2231, -0.91141), (0.2231, -0.92392, -0.3108), (-0.91141, -0.3108, 0.2697)147.93143, 6.86374, 107.86731
15generate(0.403, -0.20112, 0.89283), (-0.27223, 0.90505, 0.32675), (-0.87378, -0.37474, 0.30998)-22.52052, -4.80812, 102.72506
16generate(-0.48491, 0.403, 0.77618), (-0.64119, 0.43974, -0.62889), (-0.59476, -0.80264, 0.04517)42.14445, 83.70904, 102.89037
17generate(-0.98838, 0.08584, -0.12541), (0.08585, -0.36561, -0.9268), (-0.12541, -0.9268, 0.35399)135.58414, 57.49357, 51.91248
18generate(-0.47173, -0.64655, 0.59954), (0.30747, 0.51665, 0.79909), (-0.8264, 0.56129, -0.04492)53.30632, -73.9489, 123.81373
19generate(-0.41164, -0.71429, -0.56598), (0.90414, -0.39802, -0.15528), (-0.11436, -0.57565, 0.80966)128.66773, -47.22452, 20.24214
20generate(-0.38995, 0.40647, 0.82627), (0.37563, 0.88947, -0.26029), (-0.84074, 0.20887, -0.49953)32.67252, -6.31573, 155.62286
21generate(-0.98333, 0.1714, -0.06065), (0.1714, 0.76261, -0.62373), (-0.06065, -0.62373, -0.77928)130.86051, 31.43148, 124.78405
22generate(-0.44984, -0.72176, 0.52603), (0.89299, -0.35387, 0.27811), (-0.01458, 0.59484, 0.80371)56.90222, -75.96239, 14.27027
23generate(-0.52755, -0.71935, 0.45191), (0.30579, -0.6571, -0.68899), (0.79258, -0.22529, 0.56662)66.90514, 27.27949, -21.19838
24generate(-0.98978, 0.13667, 0.04079), (0.13667, 0.82701, 0.54532), (0.04079, 0.54532, -0.83723)124.37862, -45.78994, 122.23875
25generate(-0.56297, -0.6416, -0.52097), (-0.59766, 0.75142, -0.27959), (0.57085, 0.15396, -0.80649)135.27925, 57.19005, 86.27811
26generate(-0.45895, 0.24917, 0.85281), (0.24917, -0.88525, 0.39274), (0.85281, 0.39274, 0.3442)35.27908, -42.61027, -9.93225
27generate(0.33555, -0.35977, 0.87062), (-0.35976, -0.90309, -0.23452), (0.87062, -0.23452, -0.43247)-16.70171, 38.92641, 41.7069
28generate(0.44228, -0.42057, -0.79215), (-0.42057, -0.87736, 0.23099), (-0.79215, 0.23099, -0.56492)89.46885, 11.17858, 156.96145
29generate(0.41652, 0.75037, 0.51328), (-0.90833, 0.36704, 0.20053), (-0.03793, -0.54975, 0.83446)2.40605, 44.4176, 13.67231
30generate(0.44828, -0.89165, 0.06333), (0.68284, 0.38729, 0.61947), (-0.57687, -0.23445, 0.78246)30.9532, -85.72932, 51.64537
31generate(-0.4849, -0.64119, -0.59476), (0.403, 0.43974, -0.80263), (0.77618, -0.62889, 0.04517)135.30434, 28.78907, 15.28437
32generate(-0.3739, 0.3114, 0.87363), (0.9259, 0.07058, 0.37112), (0.0539, 0.94765, -0.31471)28.42906, -84.38522, 85.89457
33generate(-0.38994, 0.37562, -0.84074), (0.40647, 0.88947, 0.20887), (0.82627, -0.26029, -0.49952)145.95149, -40.16758, 49.09699
34generate(0.41653, -0.90833, -0.03793), (0.75037, 0.36704, -0.54976), (0.51328, 0.20053, 0.83446)39.86284, -10.5924, -21.55083
35generate(0.47521, -0.26084, 0.84032), (0.73345, 0.645, -0.21457), (-0.48603, 0.71829, 0.49782)-23.56771, -32.28851, 65.18268
36generate(0.49882, -0.25991, -0.82681), (0.74402, 0.61771, 0.2547), (0.44453, -0.74221, 0.50151)88.21125, -64.85224, 5.46764
37generate(-0.28878, 0.95739, -0.00356), (0.95739, 0.28876, -0.00478), (-0.00355, -0.00478, -0.99998)82.59694, -60.8543, 136.13267
38generate(-0.3121, 0.32348, -0.89328), (0.94394, -0.00085, -0.33011), (-0.10755, -0.94624, -0.30508)144.54716, -37.88755, 95.55674
39generate(0.5231, -0.35159, -0.77637), (0.6084, -0.48389, 0.62905), (-0.59684, -0.8014, -0.03922)83.23181, -81.62407, 108.7575
40generate(-0.31211, 0.94394, -0.10755), (0.32348, -0.00085, -0.94623), (-0.89328, -0.33011, -0.30508)91.15392, 43.62908, 145.76666
41generate(0.9849, -0.13248, 0.11149), (-0.17274, -0.79603, 0.58008), (0.01191, -0.59058, -0.80689)-6.61091, -28.37922, 122.02347
42generate(0.5231, 0.60839, -0.59684), (-0.35159, -0.48388, -0.8014), (-0.77637, 0.62906, -0.03922)71.0322, 76.92493, 120.22992
43generate(0.59628, 0.613, -0.51834), (0.613, -0.7646, -0.19905), (-0.51834, -0.19905, -0.83168)61.02105, -25.64485, 157.59219
44generate(0.49882, 0.74402, 0.44454), (-0.25991, 0.61771, -0.74221), (-0.82682, 0.25469, 0.50151)1.81839, 67.04418, 86.70924
45generate(0.99423, -0.02572, 0.10414), (-0.09087, 0.31397, 0.94507), (-0.057, -0.94908, 0.30982)-6.70753, -58.41454, 50.54273
46generate(0.47522, 0.73345, -0.48603), (-0.26084, 0.64499, 0.71829), (0.84032, -0.21457, 0.49782)66.56185, -32.14222, -19.57317
47generate(0.52634, 0.62911, 0.572), (0.62911, -0.7407, 0.23576), (0.572, 0.23576, -0.78564)-8.60164, -56.22236, 84.78798
48generate(0.99423, -0.09086, -0.057), (-0.02572, 0.31398, -0.94908), (0.10413, 0.94507, 0.30983)4.24236, 66.13664, 40.24473
49generate(0.56669, 0.66908, 0.48082), (0.69028, -0.06692, -0.72044), (-0.44986, 0.74017, -0.49978)-4.98396, 4.84557, 130.6611
50generate(-0.99795, -0.00176, -0.06399), (-0.00176, -0.99849, 0.05495), (-0.06399, 0.05495, 0.99644)132.02119, -3.62133, 4.33115
51generate(0.56669, 0.69028, -0.44986), (0.66908, -0.06691, 0.74017), (0.48083, -0.72044, -0.49977)58.2589, -93.05258, 71.18925
52generate(0.43353, -0.35889, 0.82659), (0.67935, -0.4725, -0.56146), (0.59206, 0.80495, 0.03897)-19.97068, -5.25851, 27.47092
53generate(0.403, -0.27223, -0.87377), (-0.20112, 0.90505, -0.37474), (0.89283, 0.32676, 0.30999)97.52573, 38.31606, -10.16499
54generate(-0.37391, 0.9259, 0.0539), (0.3114, 0.07058, 0.94766), (0.87363, 0.37112, -0.31471)84.13155, -84.2953, 33.51218
55generate(-0.47173, 0.30747, -0.8264), (-0.64655, 0.51665, 0.56129), (0.59954, 0.79909, -0.04492)150.20272, 3.1739, 32.69391
56generate(0.31668, -0.94787, -0.03532), (-0.26226, -0.05171, -0.96361), (0.91155, 0.31442, -0.26497)46.06545, 82.23957, 27.70836
57generate(0.9849, -0.17274, 0.01191), (-0.13247, -0.79603, -0.59058), (0.1115, 0.58008, -0.80689)0.15599, 48.59755, 115.65965
58generate(0.44828, 0.68284, -0.57687), (-0.89165, 0.38729, -0.23445), (0.06332, 0.61947, 0.78247)74.45648, 72.90991, 10.735
59generate(0.43353, 0.67935, 0.59206), (-0.35889, -0.4725, 0.80495), (0.82659, -0.56145, 0.03897)-4.03448, -31.7654, 12.48457
60generate(0.36806, -0.37153, -0.85235), (-0.92088, -0.01895, -0.38939), (0.12851, 0.92823, -0.34911)98.30245, 85.30582, 83.46339
DetailsT=1 symmetry

-
Components

#1: Protein Capsid protein VP1 / / Coat protein VP1


Mass: 81341.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Infection in NB324K cells / Source: (natural) H-1 parvovirus / References: UniProt: P03136
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE DEPOSITED THE CORRECT SEQUENCE IN THE GENBANK DATABASE ACCESSION CODE JX505432.1

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mM Tris-HCl, 150 mM NaCl, 8mM CaCl2.2H2O and 3% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0895 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0895 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. all: 782183 / Num. obs: 479478 / % possible obs: 61.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rsym value: 0.114 / Net I/σ(I): 4.9
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.4 / % possible all: 58.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementResolution: 3.2→40 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2592 22657 2.9 %
Rwork0.2563 433649 -
obs-456306 58.4 %
Solvent computationBsol: 10.7716 Å2
Displacement parametersBiso max: 128.24 Å2 / Biso mean: 61.7723 Å2 / Biso min: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.771 Å20 Å2-1.744 Å2
2---16.134 Å20 Å2
3---9.363 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4366 0 2 18 4386
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.366
X-RAY DIFFRACTIONc_mcbond_it1.1861.5
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scangle_it2.7062.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.310.387419390.3821366813862049.5
3.31-3.450.351319950.3481384304042551.8
3.45-3.60.318321000.3196400244212454
3.6-3.790.301822310.295421434437456.9
3.79-4.030.276323170.2758438404615759.1
4.03-4.340.248123390.2472451734751260.8
4.34-4.780.231324010.2296459584835961.8
4.78-5.470.233124350.2218477825021764.2
5.47-6.880.223225090.2195479955050464.5
6.88-400.210323910.2123456234801461

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more