[English] 日本語
Yorodumi
- PDB-3qeb: Crystal structure of human exonuclease 1 Exo1 (WT) in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qeb
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with DNA and Mn2+ (complex III)
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')
  • DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
  • Exonuclease 1
KeywordsHYDROLASE/DNA / exonuclease / HYDROLASE-DNA complex
Function / homology
Function and homology information


double-stranded DNA 5'-3' DNA exonuclease activity / flap endonuclease activity / single-stranded DNA 5'-3' DNA exonuclease activity / t-circle formation / 5'-flap endonuclease activity / DNA strand resection involved in replication fork processing / humoral immune response mediated by circulating immunoglobulin / Impaired BRCA2 binding to PALB2 / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...double-stranded DNA 5'-3' DNA exonuclease activity / flap endonuclease activity / single-stranded DNA 5'-3' DNA exonuclease activity / t-circle formation / 5'-flap endonuclease activity / DNA strand resection involved in replication fork processing / humoral immune response mediated by circulating immunoglobulin / Impaired BRCA2 binding to PALB2 / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching / 5'-3' exonuclease activity / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / exonuclease activity / 5'-3' DNA exonuclease activity / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / somatic hypermutation of immunoglobulin genes / mismatch repair / meiotic cell cycle / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / RNA-DNA hybrid ribonuclease activity / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / Hydrolases; Acting on ester bonds / nuclear body / DNA repair / chromatin binding / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane
Similarity search - Function
Exonuclease-1, H3TH domain / Exonuclease 1-like, PIN-like domain / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region ...Exonuclease-1, H3TH domain / Exonuclease 1-like, PIN-like domain / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / 5'-nuclease / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOrans, J. / McSweeney, E.A. / Iyer, R.R. / Hast, M.A. / Hellinga, H.W. / Modrich, P. / Beese, L.S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family.
Authors: Orans, J. / McSweeney, E.A. / Iyer, R.R. / Hast, M.A. / Hellinga, H.W. / Modrich, P. / Beese, L.S.
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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.ptnr1_auth_asym_id / _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_conn.ptnr2_label_seq_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
Z: Exonuclease 1
A: DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')
B: DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6665
Polymers46,5573
Non-polymers1102
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-26 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.406, 70.406, 182.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Exonuclease 1 / hExo1 / Exonuclease I / hExoI


Mass: 39559.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXO1, EXOI, HEX1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UQ84, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')


Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 6K, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 6K11
2MES11
3PEG 6K12
4MES12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 11100 / % possible obs: 83.3 % / Observed criterion σ(I): -3
Reflection shellResolution: 3→3.1 Å / % possible all: 53.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→31.03 Å / SU ML: 0.33 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 438 4.75 %
Rwork0.2237 --
obs0.2258 9214 93.74 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.461 Å2 / ksol: 0.302 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.2101 Å20 Å2-0 Å2
2--11.2101 Å20 Å2
3----22.4203 Å2
Refinement stepCycle: LAST / Resolution: 3→31.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 427 2 16 3159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013236
X-RAY DIFFRACTIONf_angle_d0.4124450
X-RAY DIFFRACTIONf_dihedral_angle_d16.8151251
X-RAY DIFFRACTIONf_chiral_restr0.025501
X-RAY DIFFRACTIONf_plane_restr0.001500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.43430.3251330.29142513X-RAY DIFFRACTION83
3.4343-4.32490.29121410.22993030X-RAY DIFFRACTION99
4.3249-31.03160.24651640.20573233X-RAY DIFFRACTION100
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)
10.0320.2273-0.09431.441-0.30751.1784-0.0510.27560.1811-0.4394-0.1254-0.12510.23160.02170.18780.43480.0070.10270.8096-0.36660.7404-5.312624.7232-17.3397
22.18510.1244-1.25682.9742-0.99933.22030.0541-0.02840.31371.02350.2489-0.35730.8838-0.409-0.20520.8056-0.21420.03870.5114-0.02660.5907-10.300719.23261.2595
30.4387-1.41910.16224.6466-1.11783.8289-0.92560.3060.60640.5298-0.01021.9893-0.1976-0.98410.82020.3789-0.06280.11990.7253-0.14021.6961-26.903724.63756.292
42.03190.10030.4362.53141.31064.22420.13170.2311-0.3899-0.09310.0391-0.3928-0.1084-0.404-0.11380.32930.06310.02350.3171-0.16650.3437-5.022631.237-9.8332
55.05280.05320.1644.1807-1.45240.50940.00671.43170.5641-1.11070.16050.0945-1.7269-0.6812-0.08841.26920.2953-0.02030.78940.04610.4428-13.342553.1887-16.2909
60.9195-0.91230.65861.98410.84972.4350.04-0.36650.03520.11350.2484-0.3622-0.1420.4021-0.29820.53550.0352-0.0510.5974-0.07540.42552.246936.43936.4651
74.8427-1.73145.7831.3117-0.69239.6340.76760.3543-1.50361.3260.26991.5908-0.94250.9604-0.81681.58870.41070.3380.86580.37411.1958-27.488532.5252-15.3413
81.16090.4720.94979.0072-1.78138.95390.22370.4146-0.875-0.3252.10622.03570.86370.5026-2.12951.46040.14480.07670.81040.37951.2346-27.450434.3807-16.3352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN Z AND RESID 2:28)
2X-RAY DIFFRACTION2(CHAIN Z AND RESID 29:86)
3X-RAY DIFFRACTION3(CHAIN Z AND RESID 87:130)
4X-RAY DIFFRACTION4(CHAIN Z AND RESID 131:233)
5X-RAY DIFFRACTION5(CHAIN Z AND RESID 234:276)
6X-RAY DIFFRACTION6(CHAIN Z AND RESID 277:346)
7X-RAY DIFFRACTION7(CHAIN A)
8X-RAY DIFFRACTION8(CHAIN B)

+
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