[English] 日本語
Yorodumi
- PDB-3glh: Crystal Structure of the E. coli clamp loader bound to Psi Peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3glh
TitleCrystal Structure of the E. coli clamp loader bound to Psi Peptide
Components
  • DNA polymerase III subunit delta'DNA polymerase III holoenzyme
  • DNA polymerase III subunit deltaDNA polymerase III holoenzyme
  • DNA polymerase III subunit tauDNA polymerase III holoenzyme
KeywordsTRANSFERASE / Clamp Loader / Gamma Complex / Replication / Psi / DNA replication / DNA-directed DNA polymerase / Nucleotidyltransferase / ATP-binding / Nucleotide-binding
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
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 / MOLECULAR REPLACEMENT / Resolution: 3.891 Å
AuthorsKazmirski, S.L. / Simonetta, K.R. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: The mechanism of ATP-dependent primer-template recognition by a clamp loader complex.
Authors: Simonetta, K.R. / Kazmirski, S.L. / Goedken, E.R. / Cantor, A.J. / Kelch, B.A. / McNally, R. / Seyedin, S.N. / Makino, D.L. / O'Donnell, M. / Kuriyan, J.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: DNA polymerase III subunit delta
B: DNA polymerase III subunit tau
C: DNA polymerase III subunit tau
D: DNA polymerase III subunit tau
E: DNA polymerase III subunit delta'
F: DNA polymerase III subunit delta
G: DNA polymerase III subunit tau
H: DNA polymerase III subunit tau
I: DNA polymerase III subunit tau
J: DNA polymerase III subunit delta'
K: DNA polymerase III subunit delta
L: DNA polymerase III subunit tau
M: DNA polymerase III subunit tau
N: DNA polymerase III subunit tau
O: DNA polymerase III subunit delta'


Theoretical massNumber of molelcules
Total (without water)603,40715
Polymers603,40715
Non-polymers00
Water0
1
A: DNA polymerase III subunit delta
B: DNA polymerase III subunit tau
C: DNA polymerase III subunit tau
D: DNA polymerase III subunit tau
E: DNA polymerase III subunit delta'


Theoretical massNumber of molelcules
Total (without water)201,1365
Polymers201,1365
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15990 Å2
ΔGint-64 kcal/mol
Surface area79710 Å2
MethodPISA
2
F: DNA polymerase III subunit delta
G: DNA polymerase III subunit tau
H: DNA polymerase III subunit tau
I: DNA polymerase III subunit tau
J: DNA polymerase III subunit delta'


Theoretical massNumber of molelcules
Total (without water)201,1365
Polymers201,1365
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16240 Å2
ΔGint-60 kcal/mol
Surface area79520 Å2
MethodPISA
3
K: DNA polymerase III subunit delta
L: DNA polymerase III subunit tau
M: DNA polymerase III subunit tau
N: DNA polymerase III subunit tau
O: DNA polymerase III subunit delta'


Theoretical massNumber of molelcules
Total (without water)201,1365
Polymers201,1365
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16160 Å2
ΔGint-65 kcal/mol
Surface area78830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.162, 228.494, 164.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DNA polymerase III subunit delta / DNA polymerase III holoenzyme


Mass: 38745.574 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: holA, b0640, JW0635 / Production host: Escherichia coli (E. coli) / References: UniProt: P28630, DNA-directed DNA polymerase
#2: Protein
DNA polymerase III subunit tau / DNA polymerase III holoenzyme / DNA polymerase III subunit gamma


Mass: 41803.168 Da / Num. of mol.: 9 / Fragment: UNP residues 1-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: dnaX, dnaZ, dnaZX, b0470, JW0459 / Production host: Escherichia coli (E. coli) / References: UniProt: P06710, DNA-directed DNA polymerase
#3: Protein DNA polymerase III subunit delta' / DNA polymerase III holoenzyme


Mass: 36980.484 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: holB, b1099, JW1085 / Production host: Escherichia coli (E. coli) / References: UniProt: P28631, DNA-directed DNA polymerase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 300 mM NaK Tartrate, 10% PEG 3350, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2004
RadiationMonochromator: KOHZU / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 3.891→100 Å / Num. all: 67070 / Num. obs: 65729 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.891→3.99 Å / % possible all: 94.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.891→49.621 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.87 / σ(F): 0.03 / Phase error: 41.25 / Stereochemistry target values: ML
Details: There are several close contacts because this structure is only a 4A structure
RfactorNum. reflection% reflectionSelection details
Rfree0.3614 5893 4.9 %Random
Rwork0.3593 ---
obs-64229 89.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.525 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 291.12 Å2 / Biso mean: 111.018 Å2 / Biso min: 29.92 Å2
Baniso -1Baniso -2Baniso -3
1-94.7798 Å20 Å217.6454 Å2
2--93.89 Å2-0 Å2
3---64.4952 Å2
Refinement stepCycle: LAST / Resolution: 3.891→49.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41322 0 0 0 41322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01442069
X-RAY DIFFRACTIONf_angle_d1.7957096
X-RAY DIFFRACTIONf_dihedral_angle_d19.51115639
X-RAY DIFFRACTIONf_chiral_restr0.1256648
X-RAY DIFFRACTIONf_plane_restr0.0117410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.891-3.93560.4643920.44421902X-RAY DIFFRACTION44
3.9356-3.98190.44741510.42383114X-RAY DIFFRACTION75
3.9819-4.03050.42061770.42913172X-RAY DIFFRACTION75
4.0305-4.08140.48411920.41953282X-RAY DIFFRACTION78
4.0814-4.13510.39861720.42033407X-RAY DIFFRACTION80
4.1351-4.19170.44261630.40613534X-RAY DIFFRACTION82
4.1917-4.25160.38071870.40673514X-RAY DIFFRACTION84
4.2516-4.3150.42071790.38253638X-RAY DIFFRACTION85
4.315-4.38240.41821750.3973638X-RAY DIFFRACTION85
4.3824-4.45420.3922310.39273690X-RAY DIFFRACTION88
4.4542-4.5310.37281760.38883862X-RAY DIFFRACTION90
4.531-4.61330.37911640.38173820X-RAY DIFFRACTION90
4.6133-4.7020.37322330.37693874X-RAY DIFFRACTION92
4.702-4.79790.35911910.37513942X-RAY DIFFRACTION92
4.7979-4.90210.3561840.37163940X-RAY DIFFRACTION93
4.9021-5.0160.34141920.38874044X-RAY DIFFRACTION94
5.016-5.14140.34622440.39113935X-RAY DIFFRACTION94
5.1414-5.28020.33592010.38314071X-RAY DIFFRACTION95
5.2802-5.43540.38632260.39364024X-RAY DIFFRACTION96
5.4354-5.61060.38161740.39054078X-RAY DIFFRACTION97
5.6106-5.81080.3982190.37814170X-RAY DIFFRACTION97
5.8108-6.04310.42012210.39034122X-RAY DIFFRACTION98
6.0431-6.31760.34762060.37984209X-RAY DIFFRACTION99
6.3176-6.650.41232120.36964281X-RAY DIFFRACTION99
6.65-7.06550.36442210.35944160X-RAY DIFFRACTION99
7.0655-7.60930.33122400.33144207X-RAY DIFFRACTION100
7.6093-8.37170.25281900.29524298X-RAY DIFFRACTION100
8.3717-9.57560.23972140.26894202X-RAY DIFFRACTION99
9.5756-12.03570.26722370.24664138X-RAY DIFFRACTION99
12.0357-49.6250.37462290.3094224X-RAY DIFFRACTION99

+
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