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- EMDB-75014: Cryo-EM Structure of a RAD51 filament bound by ssDNA and the XRCC... -

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Entry
Database: EMDB / ID: EMD-75014
TitleCryo-EM Structure of a RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex
Map data
Sample
  • Complex: RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
    • Protein or peptide: DNA repair protein XRCC2
    • Protein or peptide: DNA repair protein RAD51 homolog 4
    • Protein or peptide: DNA repair protein RAD51 homolog 3
    • Protein or peptide: DNA repair protein XRCC3
    • Protein or peptide: DNA repair protein RAD51 homolog 1
  • Protein or peptide: DNA repair protein RAD51 homolog 1
  • Protein or peptide: DNA repair protein RAD51 homolog 1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsPentameric / RAD51 / XRCC3 / RAD51C / RAD51D / XRCC2 / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


telomeric loop disassembly / meiotic DNA recombinase assembly / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / double-strand break repair via synthesis-dependent strand annealing / telomere maintenance via telomere trimming / female meiosis sister chromatid cohesion / resolution of mitotic recombination intermediates / presynaptic intermediate filament cytoskeleton / response to glucoside ...telomeric loop disassembly / meiotic DNA recombinase assembly / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / double-strand break repair via synthesis-dependent strand annealing / telomere maintenance via telomere trimming / female meiosis sister chromatid cohesion / resolution of mitotic recombination intermediates / presynaptic intermediate filament cytoskeleton / response to glucoside / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic recombination-dependent replication fork processing / crossover junction DNA endonuclease activity / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to cisplatin / DNA strand invasion / regulation of centrosome duplication / t-circle formation / cellular response to hydroxyurea / mitotic recombination / cellular response to camptothecin / replication-born double-strand break repair via sister chromatid exchange / lateral element / regulation of DNA damage checkpoint / DNA strand exchange activity / Impaired BRCA2 binding to PALB2 / gamma-tubulin binding / telomere maintenance via recombination / regulation of fibroblast apoptotic process / reciprocal meiotic recombination / single-stranded DNA helicase activity / centrosome cycle / positive regulation of neurogenesis / sister chromatid cohesion / 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) / HDR through Single Strand Annealing (SSA) / ATP-dependent DNA damage sensor activity / Resolution of D-loop Structures through Holliday Junction Intermediates / regulation of double-strand break repair via homologous recombination / nuclear chromosome / Impaired BRCA2 binding to RAD51 / Transcriptional Regulation by E2F6 / replication fork processing / male meiosis I / microtubule organizing center / Presynaptic phase of homologous DNA pairing and strand exchange / positive regulation of G2/M transition of mitotic cell cycle / response to X-ray / ATP-dependent activity, acting on DNA / somitogenesis / interstrand cross-link repair / condensed chromosome / DNA polymerase binding / neurogenesis / telomere maintenance / replication fork / condensed nuclear chromosome / cellular response to ionizing radiation / male germ cell nucleus / response to gamma radiation / meiotic cell cycle / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / protein-DNA complex / PML body / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / Meiotic recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / multicellular organism growth / response to toxic substance / cell junction / mitotic cell cycle / single-stranded DNA binding / site of double-strand break / Factors involved in megakaryocyte development and platelet production / double-stranded DNA binding / DNA recombination / spermatogenesis / in utero embryonic development / negative regulation of neuron apoptotic process / chromosome, telomeric region / regulation of cell cycle / response to xenobiotic stimulus / mitochondrial matrix / DNA repair / DNA damage response / chromatin binding / centrosome / chromatin / nucleolus / perinuclear region of cytoplasm
Similarity search - Function
: / DNA repair protein XRCC2 / : / : / : / RAD51D, N-terminal domain / : / : / XRCC3/RpoA-like, helix-hairpin-helix domain / DNA recombination/repair protein Rad51 ...: / DNA repair protein XRCC2 / : / : / : / RAD51D, N-terminal domain / : / : / XRCC3/RpoA-like, helix-hairpin-helix domain / DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA repair protein RAD51 homolog 3 / DNA repair protein XRCC3 / DNA repair protein XRCC2 / DNA repair protein RAD51 homolog 4 / DNA repair protein RAD51 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsRuben EA / Jia L / Olsen SK / Wasmuth EV / Rawal Y / Kwon Y / Sung P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Cryo-EM Structure of a RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex
Authors: Ruben EA / Jia L / Olsen SK / Wasmuth EV / Rawal Y / Kwon Y / Sung P
History
DepositionJan 7, 2026-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75014.png

Downloads & links

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Map

FileDownload / File: emd_75014.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 460 pix.
= 383.272 Å		0.83 Å/pix.
x 460 pix.
= 383.272 Å		0.83 Å/pix.
x 460 pix.
= 383.272 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0635
Minimum - Maximum-0.18624489 - 0.573368
Average (Standard dev.)-0.00037188924 (±0.013710529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 383.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75014_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_75014_additional_1.map
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Half map: #2

Fileemd_75014_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_75014_half_map_2.map
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Sample components

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Entire : RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 p...

EntireName: RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex
Components
  • Complex: RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
    • Protein or peptide: DNA repair protein XRCC2
    • Protein or peptide: DNA repair protein RAD51 homolog 4
    • Protein or peptide: DNA repair protein RAD51 homolog 3
    • Protein or peptide: DNA repair protein XRCC3
    • Protein or peptide: DNA repair protein RAD51 homolog 1
  • Protein or peptide: DNA repair protein RAD51 homolog 1
  • Protein or peptide: DNA repair protein RAD51 homolog 1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 p...

SupramoleculeName: RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#7, #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA repair protein RAD51 homolog 1

MacromoleculeName: DNA repair protein RAD51 homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.464375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PQPISRLEQC GINANDVKKL EEAGFHTVEA VAYAPKKELI NIKGISEAKA DKILAEAAKL VPMGFTTATE FHQRRSEIIQ ITTGSKELD KLLQGGIETG SITEMFGEFR TGKTQICHTL AVTCQLPIDR GGGEGKAMYI DTEGTFRPER LLAVAERYGL S GSDVLDNV ...String:
PQPISRLEQC GINANDVKKL EEAGFHTVEA VAYAPKKELI NIKGISEAKA DKILAEAAKL VPMGFTTATE FHQRRSEIIQ ITTGSKELD KLLQGGIETG SITEMFGEFR TGKTQICHTL AVTCQLPIDR GGGEGKAMYI DTEGTFRPER LLAVAERYGL S GSDVLDNV AYARAFNTDH QTQLLYQASA MMVESRYALL IVDSATALYR TDYSGRGELS ARQMHLARFL RMLLRLADEF GV AVVITNQ VVAQVDGAAM FAADPKKPIG GNIIAHASTT RLYLRKGRGE TRICKIYDSP CLPEAEAMFA INADGVGDA

UniProtKB: DNA repair protein RAD51 homolog 1

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Macromolecule #2: DNA repair protein RAD51 homolog 1

MacromoleculeName: DNA repair protein RAD51 homolog 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.593555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PQPISRLEQC GINANDVKKL EEAGFHTVEA VAYAPKKELI NIKGISEAKA DKILAEAAKL VPMGFTTATE FHQRRSEIIQ ITTGSKELD KLLQGGIETG SITEMFGEFR TGKTQICHTL AVTCQLPIDR GGGEGKAMYI DTEGTFRPER LLAVAERYGL S GSDVLDNV ...String:
PQPISRLEQC GINANDVKKL EEAGFHTVEA VAYAPKKELI NIKGISEAKA DKILAEAAKL VPMGFTTATE FHQRRSEIIQ ITTGSKELD KLLQGGIETG SITEMFGEFR TGKTQICHTL AVTCQLPIDR GGGEGKAMYI DTEGTFRPER LLAVAERYGL S GSDVLDNV AYARAFNTDH QTQLLYQASA MMVESRYALL IVDSATALYR TDYSGRGELS ARQMHLARFL RMLLRLADEF GV AVVITNQ VVAQVDGAAM FAADPKKPIG GNIIAHASTT RLYLRKGRGE TRICKIYDSP CLPEAEAMFA INADGVGDAK

UniProtKB: DNA repair protein RAD51 homolog 1

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Macromolecule #4: DNA repair protein XRCC2

MacromoleculeName: DNA repair protein XRCC2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.832062 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: RSSLKEIEPN LFADEDSPVH GDILEFHGPE GTGKTEMLYH LTARCILPKS EGGLEVEVLF IDTDYHFDML RLVTILEHRL SQSSEEIIK YCLGRFFLVY CSSSTHLLLT LYSLESMFCS HPSLCLLILD SLSAFYWIDR VNGGESVNLQ ESTLRKCSQC L EKLVNDYR ...String:
RSSLKEIEPN LFADEDSPVH GDILEFHGPE GTGKTEMLYH LTARCILPKS EGGLEVEVLF IDTDYHFDML RLVTILEHRL SQSSEEIIK YCLGRFFLVY CSSSTHLLLT LYSLESMFCS HPSLCLLILD SLSAFYWIDR VNGGESVNLQ ESTLRKCSQC L EKLVNDYR LVLFATTQTI MQKASSSSEE PSHASRRLCD VDIDYRPYLC KAWQQLVKHR MFFSKQDDSQ SSNQFSLVSR CL KSNSLKK HFFIIGESGV EFC

UniProtKB: DNA repair protein XRCC2

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Macromolecule #5: DNA repair protein RAD51 homolog 4

MacromoleculeName: DNA repair protein RAD51 homolog 4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.548672 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GVLRVGLCPG LTEEMIQLLR SHRIKTVVDL VSADLEEVAQ KCGLSYKALV ALRRVLLAQF SAFPVNGADL YEELKTSTAI LSTGIGSLD KLLDAGLYTG EVTEIVGGPG SGKTQVCLCM AANVAHGLQQ NVLYVDSNGG LTASRLLQLL QAKTQDEEEQ A EALRRIQV ...String:
GVLRVGLCPG LTEEMIQLLR SHRIKTVVDL VSADLEEVAQ KCGLSYKALV ALRRVLLAQF SAFPVNGADL YEELKTSTAI LSTGIGSLD KLLDAGLYTG EVTEIVGGPG SGKTQVCLCM AANVAHGLQQ NVLYVDSNGG LTASRLLQLL QAKTQDEEEQ A EALRRIQV VHAFDIFQML DVLQELRGTV AQQVTGSSGT VKVVVVDSVT AVVSPLLGGQ QREGLALMMQ LARELKTLAR DL GMAVVVT NHITRDRDSG RLKPALGRSW SFVPSTRILL DTIEGAGASG GRRMACLAKS SRQPTGFQEM VDIGTW

UniProtKB: DNA repair protein RAD51 homolog 4

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Macromolecule #6: DNA repair protein RAD51 homolog 3

MacromoleculeName: DNA repair protein RAD51 homolog 3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.021883 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MQRDLVSFPL SPAVRVKLVS AGFQTAEELL EVKPSELSKE VGISKAEALE TLQIIRRECL TNKPRYAGTS ESHKKCTALE LLEQEHTQG FIITFCSALD DILGGGVPLM KTTEICGAPG VGKTQLCMQL AVDVQIPECF GGVAGEAVFI DTEGSFMVDR V VDLATACI ...String:
MQRDLVSFPL SPAVRVKLVS AGFQTAEELL EVKPSELSKE VGISKAEALE TLQIIRRECL TNKPRYAGTS ESHKKCTALE LLEQEHTQG FIITFCSALD DILGGGVPLM KTTEICGAPG VGKTQLCMQL AVDVQIPECF GGVAGEAVFI DTEGSFMVDR V VDLATACI QHLQLIAEKH KGEEHRKALE DFTLDNILSH IYYFRCRDYT ELLAQVYLLP DFLSEHSKVR LVIVDGIAFP FR HDLDDLS LRTRLLNGLA QQMISLANNH RLAVILTNQM TTKIDRNQAL LVPALGESWG HAATIRLIFH WDRKQRLATL YKS PSQKEC TVLFQIKPQG FRD

UniProtKB: DNA repair protein RAD51 homolog 3

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Macromolecule #7: DNA repair protein XRCC3

MacromoleculeName: DNA repair protein XRCC3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.899781 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDLDLLDLNP RIIAAIKKAK LKSVKEVLHF SGPDLKRLTN LSSPEVWHLL RTASLHLRGS SILTALQLHQ QKERFPTQHQ RLSLGCPVL DALLRGGLPL DGITELAGRS SAGKTQLALQ LCLAVQFPRQ HGGLEAGAVY ICTEDAFPHK RLQQLMAQQP R LRTDVPGE ...String:
MDLDLLDLNP RIIAAIKKAK LKSVKEVLHF SGPDLKRLTN LSSPEVWHLL RTASLHLRGS SILTALQLHQ QKERFPTQHQ RLSLGCPVL DALLRGGLPL DGITELAGRS SAGKTQLALQ LCLAVQFPRQ HGGLEAGAVY ICTEDAFPHK RLQQLMAQQP R LRTDVPGE LLQKLRFGSQ IFIEHVADVD TLLECVNKKV PVLLSRGMAR LVVIDSVAAP FRCEFDSQAS APRARHLQSL GA TLRELSS AFQSPVLCIN QVTEAMEEQG AAHGPLGFWD ERVSPALGIT WANQLLVRLL ADRLREEEAA LGCPARTLRV LSA PHLPPS SCSYTISAEG VRGTPGTQSH

UniProtKB: DNA repair protein XRCC3

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Macromolecule #8: DNA repair protein RAD51 homolog 1

MacromoleculeName: DNA repair protein RAD51 homolog 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.239133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PISRLEQCGI NANDVKKLEE AGFHTVEAVA YAPKKELINI KGISEAKADK ILAEAAKLVP MGFTTATEFH QRRSEIIQIT TGSKELDKL LQGGIETGSI TEMFGEFRTG KTQICHTLAV TCQLPIDRGG GEGKAMYIDT EGTFRPERLL AVAERYGLSG S DVLDNVAY ...String:
PISRLEQCGI NANDVKKLEE AGFHTVEAVA YAPKKELINI KGISEAKADK ILAEAAKLVP MGFTTATEFH QRRSEIIQIT TGSKELDKL LQGGIETGSI TEMFGEFRTG KTQICHTLAV TCQLPIDRGG GEGKAMYIDT EGTFRPERLL AVAERYGLSG S DVLDNVAY ARAFNTDHQT QLLYQASAMM VESRYALLIV DSATALYRTD YSGRGELSAR QMHLARFLRM LLRLADEFGV AV VITNQVV AQVDGAAMFA ADPKKPIGGN IIAHASTTRL YLRKGRGETR ICKIYDSPCL PEAEAMFAIN ADGVGDA

UniProtKB: DNA repair protein RAD51 homolog 1

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Macromolecule #3: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP...

MacromoleculeName: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.951477 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)

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Macromolecule #9: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 9 / Number of copies: 11 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 73.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9omz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123502
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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