[English] 日本語
Yorodumi
- PDB-1xxh: ATPgS Bound E. Coli Clamp Loader Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xxh
TitleATPgS Bound E. Coli Clamp Loader Complex
Components
  • (DNA polymerase III, delta ...) x 2
  • DNA polymerase III subunit gammaDNA polymerase III holoenzyme
KeywordsTRANSFERASE / AAA+ ATPase clamp loader / gamma complex / DNA Polymerase III / DNA replication
Function / homology
Function and homology information


DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / DNA polymerase III, delta prime subunit / DNA polymerase III, delta subunit, C-terminal / : / DNA polymerase III, delta subunit, C terminal / DNA polymerase III subunit delta', AAA+ ATPase lid domain / DNA polymerase III subunit delta, C-terminal / Processivity clamp loader gamma complex DNA pol III C-term / DNA polymerase III, delta subunit ...Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / DNA polymerase III, delta prime subunit / DNA polymerase III, delta subunit, C-terminal / : / DNA polymerase III, delta subunit, C terminal / DNA polymerase III subunit delta', AAA+ ATPase lid domain / DNA polymerase III subunit delta, C-terminal / Processivity clamp loader gamma complex DNA pol III C-term / DNA polymerase III, delta subunit / DNA polymerase III delta, N-terminal / DNA polymerase III, delta subunit / DNA polymerase III, tau subunit, domain V / DNA polymerase III subunit tau, DnaB-binding domain IV / DNA polymerase III, tau subunit, domain V superfamily / DNA polymerase III, subunit gamma/tau, helical lid domain / DNA polymerase III subunits tau domain IV DnaB-binding / DNA polymerase III tau subunit V interacting with alpha / DNA polymerase III, subunit gamma/ tau, N-terminal / DNA polymerase III, gamma subunit, domain III / DNA polymerase III subunits gamma and tau domain III / DNA polymerase III, delta subunit / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / ClpA/B family / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / PHOSPHATE ION / DNA polymerase III subunit tau / DNA polymerase III subunit delta / DNA polymerase III subunit delta'
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.45 Å
AuthorsKazmirski, S.L. / Podobnik, M. / Weitze, T.F. / O'Donnell, M. / Kuriyan, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex
Authors: Kazmirski, S.L. / Podobnik, M. / Weitze, T.F. / O'donnell, M. / Kuriyan, J.
History
DepositionNov 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase III, delta subunit
B: DNA polymerase III subunit gamma
C: DNA polymerase III subunit gamma
D: DNA polymerase III subunit gamma
E: DNA polymerase III, delta prime subunit
F: DNA polymerase III, delta subunit
G: DNA polymerase III subunit gamma
H: DNA polymerase III subunit gamma
I: DNA polymerase III subunit gamma
J: DNA polymerase III, delta prime subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)404,35524
Polymers401,54910
Non-polymers2,80614
Water0
1
A: DNA polymerase III, delta subunit
B: DNA polymerase III subunit gamma
C: DNA polymerase III subunit gamma
D: DNA polymerase III subunit gamma
E: DNA polymerase III, delta prime subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,17812
Polymers200,7745
Non-polymers1,4037
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18100 Å2
ΔGint-88 kcal/mol
Surface area77690 Å2
MethodPISA
2
F: DNA polymerase III, delta subunit
G: DNA polymerase III subunit gamma
H: DNA polymerase III subunit gamma
I: DNA polymerase III subunit gamma
J: DNA polymerase III, delta prime subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,17812
Polymers200,7745
Non-polymers1,4037
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18560 Å2
ΔGint-91 kcal/mol
Surface area78070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.450, 106.460, 535.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThere are 2 clamp loader complexes in the asymmetric unit. One consists of chains A-E and the second consists of chains F-J

-
Components

-
DNA polymerase III, delta ... , 2 types, 4 molecules AFEJ

#1: Protein DNA polymerase III, delta subunit /


Mass: 38980.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: holA / Production host: Escherichia coli (E. coli) / References: UniProt: P28630, DNA-directed DNA polymerase
#3: Protein DNA polymerase III, delta prime subunit /


Mass: 37261.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: holB / Production host: Escherichia coli (E. coli) / References: UniProt: P28631, DNA-directed DNA polymerase

-
Protein , 1 types, 6 molecules BCDGHI

#2: Protein
DNA polymerase III subunit gamma / DNA polymerase III holoenzyme


Mass: 41510.855 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaX, dnaZ, dnaZX / Production host: Escherichia coli (E. coli) / References: UniProt: P06710, DNA-directed DNA polymerase

-
Non-polymers , 3 types, 14 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.95
Details: PEG 3350, Sodium Phosphate, Anapoe X-405, pH 7.95, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9641, 0.9797, 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2003
RadiationMonochromator: Double Crystal SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96411
20.97971
30.97951
ReflectionResolution: 3.45→100 Å / Num. obs: 73704 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.1 / Net I/σ(I): 15.1
Reflection shellResolution: 3.45→3.53 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.504 / % possible all: 86.6

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3.45→100 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.35 7430 Random
Rwork0.315 --
obs-73704 -
Refinement stepCycle: LAST / Resolution: 3.45→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27594 0 142 0 27736

+
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