[English] 日本語
Yorodumi
- PDB-3qfq: Asymmetric Assembly of Merkel Cell Polyomavirus Large T-antigen O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qfq
TitleAsymmetric Assembly of Merkel Cell Polyomavirus Large T-antigen Origin Binding Domains at the Viral Origin
Components
  • (DNA (26-MER)) x 2
  • Large T antigenLarge tumor antigen
KeywordsDNA BINDING PROTEIN/DNA / Origin binding domain / protein-DNA complex / replication / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA replication origin binding / DNA replication / ATP binding
Similarity search - Function
Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Helicase, superfamily 3, DNA virus ...Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Large T antigen
Similarity search - Component
Biological speciesMerkel cell polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9001 Å
AuthorsHarrison, C.J. / Meinke, G. / Bohm, A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Asymmetric assembly of merkel cell polyomavirus large T-antigen origin binding domains at the viral origin.
Authors: Harrison, C.J. / Meinke, G. / Kwun, H.J. / Rogalin, H. / Phelan, P.J. / Bullock, P.A. / Chang, Y. / Moore, P.S. / Bohm, A.
History
DepositionJan 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Large T antigen
B: Large T antigen
E: Large T antigen
W: DNA (26-MER)
C: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)62,9105
Polymers62,9105
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-60 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.400, 171.340, 51.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHE ASYMMETRIC UNIT CONTAINS THREE T-ANTIGEN ORIGIN BINDING DOMAIN MOLECULES BOUND TO A DNA TARGET THAT CONTAINS FOUR POTENTIAL BINDING SITES

-
Components

#1: Protein Large T antigen / Large tumor antigen


Mass: 15643.113 Da / Num. of mol.: 3 / Fragment: Origin Binding Domain (UNP Residues 308-433)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Merkel cell polyomavirus / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E2IPT4
#2: DNA chain DNA (26-MER)


Mass: 7981.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized
#3: DNA chain DNA (26-MER)


Mass: 7999.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 19-21% PEG 3350, 0.2M Lithium Acetate, 50 mM Tris pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.9→44 Å / Num. obs: 15228 / % possible obs: 91.8 % / Redundancy: 13 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 10.8
Reflection shellResolution: 2.9→3.06 Å / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.688

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NTC

2ntc


Resolution: 2.9001→38.157 Å / SU ML: 0.35 / σ(F): 1 / Phase error: 33.73 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 590 4.76 %Random
Rwork0.2251 ---
obs0.2282 12396 75.69 %-
all-15109 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.405 Å2 / ksol: 0.222 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.4117 Å2-0 Å20 Å2
2---37.9425 Å2-0 Å2
3---55.3542 Å2
Refinement stepCycle: LAST / Resolution: 2.9001→38.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 1060 0 14 3783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033969
X-RAY DIFFRACTIONf_angle_d0.715613
X-RAY DIFFRACTIONf_dihedral_angle_d17.3681485
X-RAY DIFFRACTIONf_chiral_restr0.04642
X-RAY DIFFRACTIONf_plane_restr0.002534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.19180.41671570.37933070X-RAY DIFFRACTION80
3.1918-3.65330.31851050.27181988X-RAY DIFFRACTION55
3.6533-4.60150.29311310.23042769X-RAY DIFFRACTION75
4.6015-38.15990.2471970.17753979X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.478-0.7074-0.63844.43252.74081.9187-0.35620.7156-0.1081-0.00710.15680.1141-0.0164-0.20820.00020.1436-0.04640.0470.33270.00770.107537.688-57.3728-34.9444
21.8270.43680.48423.09421.20963.0137-0.0742-0.48630.0110.69980.1197-0.0715-0.67970.00410.00020.5634-0.0014-0.13060.48890.15020.357423.48753.7913-4.4397
30.7648-0.9738-0.26912.0569-1.07842.7737-0.5251-0.30490.171.0339-0.0906-0.56370.26260.22580.00020.47020.0967-0.07010.4676-0.05570.515825.0295-29.7798-1.3244
41.0253-1.4454-1.01732.0841.36410.68690.20830.125-0.21510.0769-0.62670.9125-0.1846-0.16030.00120.51930.0182-0.11260.46380.04690.911722.9423-30.5577-24.0542
52.4104-1.70620.06832.01970.96861.02720.18330.20470.1407-0.5493-0.6276-0.5609-0.0654-0.04390.00030.5671-0.01270.07940.5004-0.01120.538821.9547-26.7515-23.0761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A)
2X-RAY DIFFRACTION2(chain B)
3X-RAY DIFFRACTION3(chain E)
4X-RAY DIFFRACTION4(chain R)
5X-RAY DIFFRACTION5(chain W)

+
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