[English] 日本語
Yorodumi
- PDB-7pa7: BK polyomavirus VP1 in complex with scFv 29B1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pa7
TitleBK polyomavirus VP1 in complex with scFv 29B1
Components
  • Major capsid protein VP1
  • scFv 29B1 antibody heavy chain
KeywordsVIRAL PROTEIN / antibody / polyomavirus / VP1 / neutralization
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein VP1
Similarity search - Component
Biological speciesHomo sapiens (human)
Betapolyomavirus hominis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHarprecht, C. / Stroeh, L.J. / Freytag, J. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: To Be Published
Title: Structural characterization of human neutralizing antibodies against JC and BK polyomavirus
Authors: Harprecht, C. / Stroeh, L.J. / Senn, L. / O'Hara, B.A. / Nagel, F. / Freytag, J. / Stiehrof, Y.D. / Atwood, W.J. / Combaluzier, B. / Stehle, T.
History
DepositionJul 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
eee: scFv 29B1 antibody heavy chain
AAA: Major capsid protein VP1
BBB: Major capsid protein VP1
CCC: Major capsid protein VP1
DDD: Major capsid protein VP1
EEE: Major capsid protein VP1
MMM: Major capsid protein VP1
NNN: Major capsid protein VP1
OOO: Major capsid protein VP1
PPP: Major capsid protein VP1
QQQ: Major capsid protein VP1
aaa: scFv 29B1 antibody heavy chain
bbb: scFv 29B1 antibody heavy chain
ccc: scFv 29B1 antibody heavy chain
ddd: scFv 29B1 antibody heavy chain
mmm: scFv 29B1 antibody heavy chain
nnn: scFv 29B1 antibody heavy chain
ooo: scFv 29B1 antibody heavy chain
ppp: scFv 29B1 antibody heavy chain
qqq: scFv 29B1 antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)572,08820
Polymers572,08820
Non-polymers00
Water13,079726
1
eee: scFv 29B1 antibody heavy chain
AAA: Major capsid protein VP1
BBB: Major capsid protein VP1
CCC: Major capsid protein VP1
DDD: Major capsid protein VP1
EEE: Major capsid protein VP1
aaa: scFv 29B1 antibody heavy chain
bbb: scFv 29B1 antibody heavy chain
ccc: scFv 29B1 antibody heavy chain
ddd: scFv 29B1 antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)286,04410
Polymers286,04410
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
MMM: Major capsid protein VP1
NNN: Major capsid protein VP1
OOO: Major capsid protein VP1
PPP: Major capsid protein VP1
QQQ: Major capsid protein VP1
mmm: scFv 29B1 antibody heavy chain
nnn: scFv 29B1 antibody heavy chain
ooo: scFv 29B1 antibody heavy chain
ppp: scFv 29B1 antibody heavy chain
qqq: scFv 29B1 antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)286,04410
Polymers286,04410
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.588, 114.614, 142.373
Angle α, β, γ (deg.)92.315, 105.996, 111.407
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody
scFv 29B1 antibody heavy chain


Mass: 26947.736 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#2: Protein
Major capsid protein VP1 / Major structural protein VP1


Mass: 30261.039 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betapolyomavirus hominis / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P03088
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium malonate (pH 5.5), 14.4% PEG 3350

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.6→49.2 Å / Num. obs: 181005 / % possible obs: 94.8 % / Redundancy: 1.8 % / Biso Wilson estimate: 34 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.17 / Net I/σ(I): 5.9
Reflection shellResolution: 2.6→2.81 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 55527 / CC1/2: 0.61 / Rrim(I) all: 0.74

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MJ1, 4KQ3

4mj1

4kq3


Resolution: 2.6→48.444 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.223 / Average fsc free: 0.8545 / Average fsc work: 0.865 / Cross valid method: FREE R-VALUE / ESU R: 0.764 / ESU R Free: 0.335
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2724 1810 1 %
Rwork0.2471 179174 -
all0.247 --
obs-180984 91.922 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.747 Å2
Baniso -1Baniso -2Baniso -3
1--1.103 Å2-0.183 Å20.491 Å2
2---1.288 Å20.287 Å2
3---1.898 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36978 0 0 726 37704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01337873
X-RAY DIFFRACTIONr_bond_other_d0.0370.01733398
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.64851569
X-RAY DIFFRACTIONr_angle_other_deg2.3761.57277534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79254822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56922.1991878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.608155716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.38815227
X-RAY DIFFRACTIONr_chiral_restr0.0640.24923
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0243139
X-RAY DIFFRACTIONr_gen_planes_other0.0070.028014
X-RAY DIFFRACTIONr_nbd_refined0.2090.26089
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2230.231517
X-RAY DIFFRACTIONr_nbtor_refined0.1660.217731
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.216921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2862
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1890.241
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.234
X-RAY DIFFRACTIONr_nbd_other0.2850.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2780.218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0440.22
X-RAY DIFFRACTIONr_mcbond_it2.6392.87419418
X-RAY DIFFRACTIONr_mcbond_other2.6392.87419417
X-RAY DIFFRACTIONr_mcangle_it4.1584.29224195
X-RAY DIFFRACTIONr_mcangle_other4.1584.29224196
X-RAY DIFFRACTIONr_scbond_it2.8482.93918455
X-RAY DIFFRACTIONr_scbond_other2.8482.93918455
X-RAY DIFFRACTIONr_scangle_it4.5074.34827374
X-RAY DIFFRACTIONr_scangle_other4.5074.34827375
X-RAY DIFFRACTIONr_lrange_it7.77853.295153107
X-RAY DIFFRACTIONr_lrange_other7.78153.29152985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.6-2.6670.3891390.362137790.362145690.6920.71795.53160.358
2.667-2.740.331380.325137180.325141620.7880.77397.83930.319
2.74-2.8190.3351350.312133050.313137000.7860.78498.10220.3
2.819-2.9060.3531310.296130350.297133960.7890.82298.28310.283
2.906-3.0010.2671280.276126300.276129650.8450.85698.40340.261
3.001-3.1060.311240.27122830.27125900.8480.86398.54650.254
3.106-3.2220.2791190.261117420.261120230.8750.87598.65260.246
3.222-3.3530.2951150.263113890.264116630.870.87398.63670.251
3.353-3.5020.289490.25349110.254112110.8880.89144.24230.239
3.502-3.6720.236870.24385470.243106890.9160.91580.77460.229
3.672-3.8690.255820.22880970.228101480.910.9380.59720.212
3.869-4.1020.25660.21565660.21596390.9190.93268.80380.2
4.102-4.3830.236890.288340.20190220.9210.94398.90270.188
4.383-4.7310.206840.18682750.18784350.9450.9599.0990.175
4.731-5.1780.193760.1976040.1977430.9510.94699.18640.176
5.178-5.7810.245700.22168740.22170030.9250.93399.15750.203
5.781-6.6590.274610.25460810.25461930.920.92399.17650.23
6.659-8.1170.328530.24351750.24452780.850.91499.05270.226
8.117-11.3220.261400.2339970.2340630.9160.92399.36010.222
11.322-48.4440.33240.2823320.2823650.8340.87999.61940.282

+
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