[English] 日本語
Yorodumi
- PDB-4ebc: Conformationally Restrained North-methanocarba-2'-deoxyadenosine ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ebc
TitleConformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota
Components
  • 5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3'
  • 5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3'
  • DNA polymerase iotaPOLI
KeywordsTRANSFERASE/DNA / polymerase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


translesion synthesis / error-prone translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck ...translesion synthesis / error-prone translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck / DNA repair / nucleoplasm / metal ion binding
Similarity search - Function
DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain ...DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
North-methanocarba-2'-deoxyadenosine triphosphate / DNA / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsEoff, R.L. / Ketkar, A. / Banerjee, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota.
Authors: Ketkar, A. / Zafar, M.K. / Banerjee, S. / Marquez, V.E. / Egli, M. / Eoff, R.L.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: DNA polymerase iota
P: 5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3'
T: 5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5558
Polymers51,8423
Non-polymers7145
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-52 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.797, 97.797, 203.628
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase iota / POLI / Eta2 / RAD30 homolog B


Mass: 47027.344 Da / Num. of mol.: 1 / Fragment: UNP residues 26-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLI, RAD30B / Plasmid: pBG101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UNA4, DNA-directed DNA polymerase

-
DNA chain , 2 types, 2 molecules PT

#2: DNA chain 5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3'


Mass: 2091.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 7-mer primer DNA
#3: DNA chain 5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3'


Mass: 2722.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 9-mer template DNA

-
Non-polymers , 4 types, 83 molecules

#4: Chemical ChemComp-0OH / North-methanocarba-2'-deoxyadenosine triphosphate


Mass: 501.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N5O11P3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 20 mM Tris-HCl, pH 7.9, 5% glycerol, 10 mM 2-mercaptoethanol, 150 mM calcium chloride, 12% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2011
RadiationMonochromator: Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.901→84.695 Å / Num. obs: 12777 / % possible obs: 95.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 24.6
Reflection shellResolution: 2.901→3 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 1.9 / % possible all: 86

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAUTOMRmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAUTOMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GV5

3gv5


Resolution: 2.901→48.899 Å / SU ML: 0.75 / Isotropic thermal model: ANISOTROPIC / σ(F): 0 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 1278 10 %
Rwork0.2063 --
obs0.211 12775 95.06 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.737 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.061 Å20 Å20 Å2
2--5.061 Å2-0 Å2
3----10.1219 Å2
Refine analyzeLuzzati sigma a obs: 0.412 Å
Refinement stepCycle: LAST / Resolution: 2.901→48.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 325 40 78 3365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173365
X-RAY DIFFRACTIONf_angle_d1.4924616
X-RAY DIFFRACTIONf_dihedral_angle_d19.1571292
X-RAY DIFFRACTIONf_chiral_restr0.085542
X-RAY DIFFRACTIONf_plane_restr0.006530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.901-3.01730.41051240.29651117X-RAY DIFFRACTION86
3.0173-3.15460.30081330.25211194X-RAY DIFFRACTION91
3.1546-3.32090.26931340.20951209X-RAY DIFFRACTION92
3.3209-3.52890.28931400.21451251X-RAY DIFFRACTION95
3.5289-3.80130.25071410.21641273X-RAY DIFFRACTION97
3.8013-4.18370.28351430.19671292X-RAY DIFFRACTION97
4.1837-4.78860.1941490.1681334X-RAY DIFFRACTION99
4.7886-6.03140.27211500.21381354X-RAY DIFFRACTION98
6.0314-48.90540.21961640.19831473X-RAY DIFFRACTION99
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)
10.16290.1107-0.14170.8843-0.51861.03030.0410.02810.02430.2542-0.2176-0.5666-0.53070.2606-0.04090.529-0.1986-0.09280.46770.07810.564699.1574-16.8799224.8018
21.03170.6843-0.08340.92120.760.86310.0163-0.04560.0736-0.1706-0.18450.0452-0.0445-0.196800.38290.03590.04680.3571-0.03140.320781.7366-16.6678208.6886
30.4363-0.1363-0.14270.3147-0.16230.1104-0.0926-0.1111-0.7587-0.0495-0.1275-0.75780.37810.1115-0.00050.6674-0.07040.16280.5093-0.06210.75898.3102-37.6061201.2618
40.02490.431-0.00111.1617-0.08040.65910.4937-0.4998-0.52890.165-0.2652-0.25460.4736-0.4116-0.20840.7177-0.3382-0.11630.64470.21450.655390.3928-40.9611235.2371
50.1255-0.06760.32250.2464-0.06450.54580.1442-0.7368-0.5727-0.4085-0.4861-0.1387-0.2413-0.4547-0.09170.6639-0.15750.08270.48220.18131.050194.128-41.0484219.1591
60.0525-0.0884-0.00960.1209-0.13910.15760.157-0.2722-1.2664-0.4884-0.1937-0.89860.31950.28410.00560.5814-0.29380.04010.57280.10240.610392.3517-36.3562222.863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 26:99)
2X-RAY DIFFRACTION2chain 'A' and (resseq 100:232)
3X-RAY DIFFRACTION3chain 'A' and (resseq 233:286)
4X-RAY DIFFRACTION4chain 'A' and (resseq 287:414)
5X-RAY DIFFRACTION5chain 'P' and (resseq 1:7)
6X-RAY DIFFRACTION6chain 'T' and (resseq 3:11)

+
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