[English] 日本語
Yorodumi
- PDB-4a09: Structure of hsDDB1-drDDB2 bound to a 15 bp CPD-duplex (purine at... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a09
TitleStructure of hsDDB1-drDDB2 bound to a 15 bp CPD-duplex (purine at D-1 position) at 3.1 A resolution (CPD 2)
Components
  • (DNA DAMAGE-BINDING PROTEIN ...) x 2
  • 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3'
  • 5'-D(*GP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*GP)-3'
KeywordsDNA-BINDING PROTEIN/DNA / DNA-BINDING PROTEIN-DNA COMPLEX / DNA DAMAGE REPAIR / DDB
Function / homology
Function and homology information


Dual Incision in GG-NER / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Neddylation / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition ...Dual Incision in GG-NER / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Neddylation / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / site of DNA damage / ectopic germ cell programmed cell death / positive regulation of viral genome replication / response to UV / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Wnt signaling pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Helix Hairpins - #3280 / DNA damage-binding protein 2 / DNA polymerase; domain 1 - #910 / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase ...Helix Hairpins - #3280 / DNA damage-binding protein 2 / DNA polymerase; domain 1 - #910 / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / DNA polymerase; domain 1 / Helix Hairpins / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA damage-binding protein 1 / DNA damage-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
DANIO RERIO (zebrafish)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsScrima, A. / Fischer, E.S. / Iwai, S. / Gut, H. / Thoma, N.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation
Authors: Scrima, A. / Fischer, E.S. / Iwai, S. / Gut, H. / Thoma, N.H.
History
DepositionSep 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval ..._entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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 DAMAGE-BINDING PROTEIN 1
B: DNA DAMAGE-BINDING PROTEIN 2
G: 5'-D(*GP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*GP)-3'
H: 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,2145
Polymers182,1744
Non-polymers401
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-43.3 kcal/mol
Surface area63920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.650, 122.940, 154.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA DAMAGE-BINDING PROTEIN ... , 2 types, 2 molecules AB

#1: Protein DNA DAMAGE-BINDING PROTEIN 1 / DDB P127 SUBUNIT / DNA DAMAGE-BINDING PROTEIN A / DDBA / DAMAGE-SPECIFIC DNA-BINDING PROTEIN 1 / ...DDB P127 SUBUNIT / DNA DAMAGE-BINDING PROTEIN A / DDBA / DAMAGE-SPECIFIC DNA-BINDING PROTEIN 1 / HBV X-ASSOCIATED PROTEIN 1 / XAP-1 / UV-DAMAGED DNA-BINDING FACTOR / UV-DAMAGED DNA-BINDING PROTEIN 1 / UV-DDB 1 / XPE-BINDING FACTOR / XPE-BF / XERODERMA PIGMENTOSUM GROUP E-COMPLEMENTING PROTEIN / XPCE


Mass: 129336.867 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q16531
#2: Protein DNA DAMAGE-BINDING PROTEIN 2 / DAMAGE-SPECIFIC DNA-BINDING PROTEIN 2


Mass: 43418.102 Da / Num. of mol.: 1 / Fragment: RESIDUES 60-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q2YDS1

-
DNA chain , 2 types, 2 molecules GH

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


Mass: 4698.073 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DAMAGED STRAND. CONTAINS CYCLOBUTANE PYRIMIDINE DIMER (CPD)
Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3'


Mass: 4721.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: UNDAMAGED STRAND / Source: (synth.) SYNTHETIC CONSTRUCT (others)

-
Non-polymers , 2 types, 23 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 194 TO ALA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.07 % / Description: NONE
Crystal growpH: 5.3 / Details: 100 MM MES, 15 MM NAOH, 21% PEG 200, pH 5.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 39092 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 16
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.5 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EI1

3ei1


Resolution: 3.1→48.27 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.828 / SU B: 25.208 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.554 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.30753 1955 5 %RANDOM
Rwork0.24519 ---
obs0.24833 37137 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.702 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2---2.96 Å20 Å2
3---4.86 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11485 605 1 22 12113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02212399
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9962.02216939
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19451453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78424.551534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.538152044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2821563
X-RAY DIFFRACTIONr_chiral_restr0.0630.21933
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219091
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2621.57248
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.476211744
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.39435151
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.7724.55193
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 141 -
Rwork0.318 2673 -
obs--100 %

+
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