[English] 日本語
Yorodumi
- PDB-7kzs: Structure of the human fanconi anaemia Core-UBE2T-ID-DNA complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kzs
TitleStructure of the human fanconi anaemia Core-UBE2T-ID-DNA complex in open state
Components
  • (DNA (25-MER)) x 2
  • (Fanconi anemia core complex-associated protein ...) x 2
  • (Fanconi anemia group ...) x 7
  • E3 ubiquitin-protein ligase FANCL
  • Fanconi anemia, complementation group I
  • Ubiquitin-conjugating enzyme E2 T
KeywordsLIGASE/DNA / Complex / LIGASE / LIGASE-DNA complex
Function / homology
Function and homology information


regulation of germ cell proliferation / regulation of CD40 signaling pathway / protein K29-linked ubiquitination / Fanconi anaemia nuclear complex / protein K27-linked ubiquitination / regulation of regulatory T cell differentiation / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / male meiotic nuclear division / gamete generation ...regulation of germ cell proliferation / regulation of CD40 signaling pathway / protein K29-linked ubiquitination / Fanconi anaemia nuclear complex / protein K27-linked ubiquitination / regulation of regulatory T cell differentiation / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / male meiotic nuclear division / gamete generation / replication-born double-strand break repair via sister chromatid exchange / neuronal stem cell population maintenance / protein K6-linked ubiquitination / protein K11-linked ubiquitination / brain morphogenesis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / E2 ubiquitin-conjugating enzyme / myeloid cell homeostasis / negative regulation of double-strand break repair via homologous recombination / positive regulation of double-strand break repair via homologous recombination / female gonad development / ubiquitin conjugating enzyme activity / protein monoubiquitination / spermatid development / germ cell development / protein K63-linked ubiquitination / protein K48-linked ubiquitination / protein autoubiquitination / interstrand cross-link repair / DNA polymerase binding / ovarian follicle development / condensed chromosome / removal of superoxide radicals / mitochondrion organization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / nucleotide-excision repair / Fanconi Anemia Pathway / response to gamma radiation / TP53 Regulates Transcription of DNA Repair Genes / response to radiation / PKR-mediated signaling / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / male gonad development / ubiquitin protein ligase activity / cellular response to oxidative stress / nuclear envelope / chromosome / regulation of cell population proliferation / regulation of inflammatory response / protein-containing complex assembly / damaged DNA binding / nuclear body / DNA repair / intracellular membrane-bounded organelle / centrosome / DNA damage response / chromatin binding / ubiquitin protein ligase binding / chromatin / nucleolus / mitochondrion / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fanconi anaemia group C protein / Fanconi anemia-associated protein of 100kDa / Fanconi anemia group B protein / Fanconi anemia group G protein / Fanconi anaemia group C protein / Fanconi anemia-associated / Fanconi Anaemia group E protein, C-terminal / Fanconi anemia group F protein / FANCF, C-terminal domain superfamily / Fanconi anemia group E protein ...Fanconi anaemia group C protein / Fanconi anemia-associated protein of 100kDa / Fanconi anemia group B protein / Fanconi anemia group G protein / Fanconi anaemia group C protein / Fanconi anemia-associated / Fanconi Anaemia group E protein, C-terminal / Fanconi anemia group F protein / FANCF, C-terminal domain superfamily / Fanconi anemia group E protein / Fanconi anemia group F protein (FANCF) / Fanconi Anaemia group E protein FANCE / Fanconi anaemia group A protein / Fanconi anaemia group A protein, N-terminal domain / Fanconi anaemia group A protein / Fanconi anaemia group A protein N terminus / FANCL, UBC-like domain 2 / FANCL, UBC-like domain 3 / Fanconi anemia complex, subunit FancL, WD-repeat containing domain / E3 ubiquitin-protein ligase FANCL / FANCL C-terminal domain / FANCL, UBC-like domain 3 superfamily / FANCL UBC-like domain 1 / FANCL C-terminal domain / FANCL UBC-like domain 2 / FANCL UBC-like domain 3 / FANCL C-terminal domain / Fanconi anemia group I protein / FANCI solenoid 1 cap / FANCI solenoid 1 domain / FANCI helical domain 1 / FANCI helical domain 2 / FANCI solenoid 3 domain / FANCI solenoid 4 domain / FANCI solenoid 2 domain / FANCI solenoid 1 cap / FANCI solenoid 1 / FANCI solenoid 2 / FANCI solenoid 3 / FANCI solenoid 4 / FANCI helical domain 1 / FANCI helical domain 2 / Fanconi anaemia protein FANCD2 / Fanconi anaemia protein FancD2 nuclease / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Fanconi anemia, complementation group I / Fanconi anemia group G protein / Fanconi anemia group A protein / Fanconi anemia group C protein / Fanconi anemia core complex-associated protein 100 / Fanconi anemia group B protein / Fanconi anemia group D2 protein / Fanconi anemia group E protein ...DNA / DNA (> 10) / Fanconi anemia, complementation group I / Fanconi anemia group G protein / Fanconi anemia group A protein / Fanconi anemia group C protein / Fanconi anemia core complex-associated protein 100 / Fanconi anemia group B protein / Fanconi anemia group D2 protein / Fanconi anemia group E protein / Ubiquitin-conjugating enzyme E2 T / Fanconi anemia group F protein / E3 ubiquitin-protein ligase FANCL
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang, S.L. / Pavletich, N.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structure of the FA core ubiquitin ligase closing the ID clamp on DNA.
Authors: Shengliu Wang / Renjing Wang / Christopher Peralta / Ayat Yaseen / Nikola P Pavletich /
Abstract: The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks. Central to the pathway is the FA core complex, a ubiquitin ligase of nine subunits that monoubiquitinates ...The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks. Central to the pathway is the FA core complex, a ubiquitin ligase of nine subunits that monoubiquitinates the FANCI-FANCD2 (ID) DNA clamp. The 3.1 Å structure of the 1.1-MDa human FA core complex, described here, reveals an asymmetric assembly with two copies of all but the FANCC, FANCE and FANCF subunits. The asymmetry is crucial, as it prevents the binding of a second FANCC-FANCE-FANCF subcomplex that inhibits the recruitment of the UBE2T ubiquitin conjugating enzyme, and instead creates an ID binding site. A single active site then ubiquitinates FANCD2 and FANCI sequentially. We also present the 4.2-Å structures of the human core-UBE2T-ID-DNA complex in three conformations captured during monoubiquitination. They reveal the core-UBE2T complex remodeling the ID-DNA complex, closing the clamp on the DNA before ubiquitination. Monoubiquitination then prevents clamp opening after release from the core.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-23088
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fanconi anemia group A protein
B: Fanconi anemia group B protein
C: Fanconi anemia group C protein
E: Fanconi anemia group E protein
F: Fanconi anemia group F protein
G: Fanconi anemia group G protein
H: Fanconi anemia group G protein
L: E3 ubiquitin-protein ligase FANCL
O: Fanconi anemia group B protein
P: Fanconi anemia core complex-associated protein 100
Q: Fanconi anemia core complex-associated protein 100
S: Fanconi anemia group A protein
W: Fanconi anemia core complex-associated protein 20
M: E3 ubiquitin-protein ligase FANCL
X: Ubiquitin-conjugating enzyme E2 T
U: Fanconi anemia, complementation group I
V: Fanconi anemia group D2 protein
Y: DNA (25-MER)
Z: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,506,42724
Polymers1,506,10019
Non-polymers3275
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Fanconi anemia group ... , 7 types, 10 molecules ASBOCEFGHV

#1: Protein Fanconi anemia group A protein / Protein FACA


Mass: 165513.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCA, FAA, FACA, FANCH / Production host: Homo sapiens (human) / References: UniProt: O15360
#2: Protein Fanconi anemia group B protein / Protein FACB / Fanconi anemia-associated polypeptide of 95 kDa / FAAP95


Mass: 100640.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCB / Production host: Homo sapiens (human) / References: UniProt: Q8NB91
#3: Protein Fanconi anemia group C protein / Protein FACC


Mass: 66290.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCC, FAC, FACC / Production host: Homo sapiens (human) / References: UniProt: Q00597
#4: Protein Fanconi anemia group E protein / Protein FACE


Mass: 61026.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCE, FACE / Production host: Homo sapiens (human) / References: UniProt: Q9HB96
#5: Protein Fanconi anemia group F protein / Protein FACF


Mass: 45108.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCF / Production host: Homo sapiens (human) / References: UniProt: Q9NPI8
#6: Protein Fanconi anemia group G protein / Protein FACG / DNA repair protein XRCC9


Mass: 70873.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCG, XRCC9 / Production host: Homo sapiens (human) / References: UniProt: O15287
#12: Protein Fanconi anemia group D2 protein / Protein FACD2


Mass: 164325.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCD2, FACD / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BXW9

-
Protein , 3 types, 4 molecules LMXU

#7: Protein E3 ubiquitin-protein ligase FANCL / Fanconi anemia group L protein / Fanconi anemia-associated polypeptide of 43 kDa / FAAP43 / RING- ...Fanconi anemia group L protein / Fanconi anemia-associated polypeptide of 43 kDa / FAAP43 / RING-type E3 ubiquitin transferase FANCL


Mass: 45203.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCL, PHF9 / Production host: Homo sapiens (human)
References: UniProt: Q9NW38, RING-type E3 ubiquitin transferase
#10: Protein Ubiquitin-conjugating enzyme E2 T / Cell proliferation-inducing gene 50 protein / E2 ubiquitin-conjugating enzyme T / Ubiquitin carrier ...Cell proliferation-inducing gene 50 protein / E2 ubiquitin-conjugating enzyme T / Ubiquitin carrier protein T / Ubiquitin-protein ligase T


Mass: 22553.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2T, HSPC150, PIG50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NPD8, E2 ubiquitin-conjugating enzyme
#11: Protein Fanconi anemia, complementation group I /


Mass: 149512.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B7ZMF2

-
Fanconi anemia core complex-associated protein ... , 2 types, 3 molecules PQW

#8: Protein Fanconi anemia core complex-associated protein 100 / Fanconi anemia-associated protein of 100 kDa


Mass: 96513.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAAP100, C17orf70 / Production host: Homo sapiens (human) / References: UniProt: Q0VG06
#9: Protein/peptide Fanconi anemia core complex-associated protein 20


Mass: 4041.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

-
DNA chain , 2 types, 2 molecules YZ

#13: DNA chain DNA (25-MER)


Mass: 18036.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#14: DNA chain DNA (25-MER)


Mass: 17716.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 1 types, 5 molecules

#15: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN
Sequence detailsThe complete sequence of FAAP20 is MEAARRPRLGLSRRRPPPAGGPSGGRPWFLLGGDERERLWAELLRTVSPELILDHEVPSL ...The complete sequence of FAAP20 is MEAARRPRLGLSRRRPPPAGGPSGGRPWFLLGGDERERLWAELLRTVSPELILDHEVPSL PAFPGQEPRCGPEPTEVFTVGPKTFSWTPFPPDLWGPGRSYRLLHGAGGHLESPARSLPQ RPAPDPCRAPRVEQQPSVEGAAALRSCPMCQKEFAPRLTQLDVDSHLAQCLAESTEDVTW

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human Fanconi Anaemia Core-UBE2T-ID-DNA complex / Type: COMPLEX / Entity ID: #1-#14 / Source: RECOMBINANT
Molecular weightValue: 1.4 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtrisC4H11NO31
2100 mMsodium chlorideNaClSodium chloride1
35 mMmagnesium chlorideMgCl21
45 mMAdenosine triphosphateC10H16N5O13P31
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 36.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40749 / Symmetry type: POINT
RefinementResolution: 4.2→20 Å / Cor.coef. Fo:Fc: 0.855 / SU B: 87.763 / SU ML: 0.482 / ESU R: 0.817
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.33021 --
obs0.33021 605838 99.08 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å2-0.96 Å2-1.46 Å2
2---1.03 Å2-4.72 Å2
3----1.95 Å2
Refinement stepCycle: 1 / Total: 87804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.01389671
ELECTRON MICROSCOPYr_bond_other_d0.0340.01786668
ELECTRON MICROSCOPYr_angle_refined_deg1.8721.626121696
ELECTRON MICROSCOPYr_angle_other_deg2.3831.581199678
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.585510913
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.73622.0794362
ELECTRON MICROSCOPYr_dihedral_angle_3_deg19.1591515728
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.87115580
ELECTRON MICROSCOPYr_chiral_restr0.0890.211648
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0298828
ELECTRON MICROSCOPYr_gen_planes_other0.0090.0220083
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it3.5611.24143976
ELECTRON MICROSCOPYr_mcbond_other3.5611.24143975
ELECTRON MICROSCOPYr_mcangle_it6.37554781
ELECTRON MICROSCOPYr_mcangle_other6.37554782
ELECTRON MICROSCOPYr_scbond_it2.46711.67445695
ELECTRON MICROSCOPYr_scbond_other2.46711.67345694
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other4.88466915
ELECTRON MICROSCOPYr_long_range_B_refined11.36199832
ELECTRON MICROSCOPYr_long_range_B_other11.36199833
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 4.2→4.304 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.421 43264 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON MICROSCOPY

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)
11.56420.98350.38064.12030.94960.87260.2131-0.45010.16840.4077-0.131-0.04420.1441-0.0931-0.08210.56240.04720.12591.10140.42440.966100.7013195.275864.8402
24.2159-1.9597-0.15233.89920.37542.56770.0344-0.21750.2171-0.0949-0.40210.5980.0299-0.47870.36780.35920.07970.12031.01050.3261.277273.7885179.175848.4427
32.2912-1.6182-0.39173.2189-0.53372.16270.1309-0.1158-0.022-0.2479-0.14190.7983-0.0243-0.48040.0110.44860.1057-0.21721.06210.21091.576753.3919181.927339.4177
45.6832-2.40892.56864.53832.09114.6224-0.0191-0.0651-0.2530.150.19470.17080.42440.0005-0.17560.70240.11090.10650.71720.44250.934393.8999160.200747.7683
51.3487-0.1732-1.44546.069-0.33981.59580.362-0.11460.42260.09880.0459-0.3812-0.4170.1355-0.40790.5579-0.04070.26870.77370.22231.3539111.1495215.025654.2879
66.3297-5.1061-0.53045.77960.4391.73370.33780.35480.4646-0.2895-0.1858-0.2876-0.04190.0577-0.15190.30870.1340.29180.79210.46551.1964140.34188.320343.1089
71.58932.05510.67036.17051.942811.7846-0.3616-0.46480.08840.3274-0.4292-0.3558-0.5389-0.09990.79080.47450.4271-0.15250.81020.42281.0269112.5565143.62768.5024
89.197-3.7033.23098.9555-0.64183.23940.28550.3725-0.43520.342-0.04260.69370.2720.1185-0.2430.5260.28250.18770.84650.34920.746986.3476134.990438.708
97.9446-1.24510.04447.3772.52630.8973-0.3630.54980.0334-1.09770.3220.152-0.41110.09280.0411.09560.2465-0.30181.00690.09340.758876.249163.325220.2624
104.25544.0741.87094.8970.80421.8172-0.57681.1792-1.8584-1.67721.0795-2.04150.77110.49-0.50271.81460.18310.19521.8827-0.00031.6912107.4567169.961727.5976
117.1229-2.3963.87296.6571-0.41228.6576-0.4098-0.0708-0.05320.71370.11060.07410.0574-0.61340.29920.66280.24510.57810.87750.47630.711280.481190.6793159.422
129.8171-0.9471.23176.87374.2149.7334-0.39540.5241-0.5064-0.9062-0.35220.49680.4333-1.0510.74760.92170.01780.6660.6480.33871.3011117.334787.541180.3839
131.61021.6699-2.39656.4205-0.30495.2341-0.219-0.2619-0.34520.0477-0.6186-0.35260.03730.80490.83760.57550.20860.1491.3290.72821.3614120.185196.4385213.9515
141.5259-0.10020.22620.68890.06450.0475-0.1013-0.46850.46861.01770.0798-0.41240.09360.01510.02151.81450.21720.04111.70610.34761.724999.814591.717225.6001
151.73940.43370.2693.888-1.72510.94720.4484-0.2425-0.58450.1971-0.3023-0.45970.0706-0.1123-0.14610.7075-0.0096-0.16141.19920.82230.9535177.1491109.705864.8009
162.023-0.46660.87675.88311.73031.0862-0.08430.03480.3070.2112-0.1396-0.38280.1009-0.00390.22390.52140.17640.30740.95760.60050.9399168.6083155.970947.9965
171.00680.8186-0.52120.7598-0.50880.3654-0.00910.5208-0.2966-0.09410.13-0.07160.0023-0.105-0.12090.69370.3813-0.11851.73510.2741.4824220.2707127.033870.3236
180.683-0.509-0.54010.52130.44660.4586-0.0895-0.06470.1019-0.07040.3638-0.1331-0.0090.0347-0.27440.71120.0818-0.02461.72740.80411.4546258.6275131.308698.3073
194.1371-2.79473.82012.1756-2.16755.8642-0.3525-0.1960.3180.14810.0475-0.1711-1.00230.01430.3050.79050.11290.10581.0460.73081.2155261.6326154.0199156.866
200.53090.3316-0.82162.1851-1.17423.8994-0.2010.3051-0.1317-0.2554-0.1389-0.0791-0.1899-0.04070.33990.52560.290.19681.32350.65630.982246.7037126.2194139.772
211.6851.35780.64462.05510.33052.40440.3539-0.326-0.04150.2589-0.0361-0.50660.1683-0.0439-0.31780.59110.12820.1531.47240.8841.0652269.5374130.8676181.2963
221.7402-0.30261.19150.1659-0.20660.8216-0.1623-0.05050.09150.10980.0461-0.3037-0.22330.02250.11620.8632-0.31440.22291.77160.75941.3705287.6679154.6736176.925
233.30492.7971-0.83095.3751-0.79921.1998-0.1645-0.13080.16960.9698-0.1233-0.82670.01230.26290.28780.51770.3377-0.09841.20631.14451.6047145.763781.1867140.4934
245.63572.5435-1.974.2878-1.54783.5367-0.033-0.39370.2418-0.3142-0.13810.71590.2452-0.51830.17120.14190.36160.06521.84160.54431.1592185.769100.8707164.6624
250.78660.39181.20817.80230.97492.6870.09070.0407-0.4197-0.24270.1315-0.8162-0.54650.1377-0.22220.58890.0887-0.15850.59330.61091.6518157.2565126.2148126.3577
260.1884-0.3852-0.6631.79243.63277.52740.2176-0.1207-0.3765-0.00520.12050.03980.2136-0.0025-0.33810.830.1408-0.34180.65030.68241.579156.1902152.1322151.6073
270.9594-0.5197-1.62690.3040.89192.83350.3204-0.4640.2553-0.23370.1469-0.0995-0.3310.6776-0.46731.37040.27670.26941.22670.35370.991159.6077165.3147178.088
282.654-0.0325-0.08353.69820.25560.0428-0.2906-0.2150.3853-0.24950.14810.2631-0.0510.13430.14250.87320.2989-0.04331.2470.64880.9683230.0731149.3384177.7865
293.39781.0206-0.32542.54060.43330.79390.1135-0.6092-0.44850.1586-0.2468-0.40450.32370.05310.13330.39340.37620.16511.39010.80541.139244.4982103.4844175.2054
305.3863.9908-1.42083.4766-1.25661.50120.15270.4829-0.63770.19310.1291-0.13690.1206-0.4134-0.28180.33050.33870.17361.25870.77641.4831220.751887.9212165.7313
313.7494-0.7639-1.02275.42321.46830.86480.01960.2499-0.70620.29690.08130.2590.046-0.2862-0.10080.62890.31660.21050.91020.52430.8846118.000990.923747.3974
322.55610.95715.05420.90653.487517.8443-0.21780.069-0.16810.1519-0.17780.26510.1537-0.01360.39550.7810.35770.19240.7360.30590.9372108.4361124.29158.5658
334.58460.06481.4347.2415-0.17013.29870.04930.46190.2624-0.5997-0.2027-0.45780.30570.5410.15340.3960.29650.38960.98190.70560.8805122.953105.928296.7622
346.32551.2567-0.42574.0801-1.959810.5360.4244-0.004-0.4808-0.0217-0.2417-0.704-0.09660.1836-0.18270.26120.35730.09270.71310.55381.093128.009792.1719119.3795
353.4496-0.9255-1.2587.23112.37442.9431-0.5726-0.35670.68170.44280.4835-0.9644-0.18690.18560.08910.68030.1299-0.35140.7740.47031.4221132.0887128.7705129.7186
364.13171.64480.17833.47610.29260.4097-0.01810.3004-0.2542-0.04620.1223-0.021-0.01090.0723-0.10420.38480.26630.13560.98370.4640.9435144.0927119.635945.7291
370.6553-0.2950.05464.0939-1.90519.0397-0.24460.07230.77010.0270.3650.2503-0.2014-0.3-0.12040.27640.26530.00450.92880.59091.4564109.5052120.2562104.0964
384.46642.67492.09276.44572.07561.4902-0.2683-0.78371.25840.4543-0.40240.1766-0.3903-0.8460.67070.81040.73680.0861.15750.19661.5665111.3134.72127.7596
391.6658-0.50230.29883.195-0.76732.896-0.12940.2494-0.53060.07570.0027-0.10530.1681-0.05280.12670.15030.34020.28711.26070.8941.2009114.949136.4155162.4942
4012.9683-5.978712.61244.4541-6.674613.21380.2723-0.4559-0.2262-0.47880.0108-0.20230.7233-0.4331-0.28310.5250.50360.31151.0560.61360.7294100.351379.0075155.0226
417.65962.3138-0.9144.10581.48584.70550.10060.0884-0.4116-0.03350.02910.26750.8-0.0688-0.12970.53710.28420.27240.7680.6120.907896.824581.9577114.9615
422.96520.84411.85337.2252-2.98475.2726-0.86540.6333-0.14-1.23650.58980.73190.86310.20820.27570.94350.04550.30461.05980.48110.950999.434784.472988.3688
430.1330.1370.08260.2278-0.09230.6991-0.23360.0082-0.0306-0.23370.00330.1736-0.24130.2340.23040.5414-0.08880.01951.33260.46322.212463.314293.671794.2314
443.35610.6095-1.41014.8294-0.22473.340.0946-0.2069-0.50850.6501-0.06460.5349-0.42270.0892-0.030.33250.450.47091.14720.99881.123984.197455.4896174.725
451.2183-0.28971.76424.4715-3.00677.6643-0.010.12530.49580.0894-0.36230.53560.2803-0.41390.37240.2070.23110.3391.06860.49461.198788.1656102.0512117.7395
469.40491.6591-1.63342.12841.13691.5348-0.7260.2081.3069-0.48270.01461.4989-0.278-0.36850.71140.25830.3976-0.16881.81141.27152.227966.767112.3823104.2426
476.06682.0795-1.68921.96330.51572.3371-0.1609-0.0074-0.3120.44330.24880.11570.3274-0.2986-0.0880.8739-0.3347-0.05641.07520.73181.112458.336394.2503256.9146
486.0921.0048-2.80774.8034-2.23952.80530.4785-0.5054-0.00720.1064-0.18170.0862-0.1304-0.0432-0.29680.6306-0.11520.11891.24450.42540.709386.6495113.6729247.1126
492.78112.23722.10734.34780.27783.3581-0.6678-0.1743-0.2368-0.09040.3905-0.2241-0.7148-0.22060.27720.64440.04560.29941.36190.36680.841103.0069126.8092237.686
504.6241-3.2773-2.84792.39071.565910.6748-0.3247-0.0563-0.30920.2790.30010.2746-0.30460.00750.02460.5275-0.25180.37561.49570.11260.7629111.0452124.4605223.4004
5112.96650.4834-0.86714.9756-1.36081.84030.277-1.10010.1044-0.5587-0.166-0.52740.23690.18-0.1110.7562-0.24920.15511.41820.05920.4666120.2251124.9457205.0956
524.7020.6284-0.45845.83680.66392.1142-0.00531.0456-0.892-0.4595-0.06130.4346-0.39250.83090.06650.6107-0.08860.3161.6216-0.03240.6148140.0105133.2204199.6492
536.4289-0.55010.21232.06890.8981.2718-0.91780.29960.30340.19880.69790.3362-0.80571.07240.21991.3229-0.2820.231.58580.34990.4878148.6429148.4426207.7437
546.70883.01942.94561.45370.83655.0171-0.09570.0505-0.23680.03610.1661-0.1652-0.34910.0428-0.07040.82050.22050.31621.31450.23370.6652145.0579139.4739228.6101
551.91230.42861.03260.3270.87813.02290.2055-1.2950.2336-0.19-0.31330.0746-0.2160.04320.10780.80810.22540.06421.9654-0.02420.7664136.6964144.109249.1774
560.3355-1.1816-0.15086.04930.80760.1640.019-0.36740.13730.0452-0.03240.3628-0.2439-0.06240.01341.15990.09690.35551.5058-0.46390.8946116.9328152.5831259.2138
571.79830.99281.40450.6830.89021.25620.8808-0.30020.07980.3579-0.5042-0.13780.4947-0.4103-0.37661.25250.29260.53721.1903-0.08651.5247101.4254156.2051261.6808
587.88692.4991-2.64991.20380.55577.67070.5410.46070.10730.10060.2146-0.4556-0.2058-0.2073-0.75570.16060.19790.26311.09430.19981.1547136.6746124.2922172.5471
595.9787-0.78332.0261.00822.44238.918-0.15680.54380.2336-0.07830.08530.0501-0.60450.54690.07150.77890.10970.27931.13830.45370.6226113.2505129.9664179.7414
6010.07990.5519-3.62639.54080.78023.59720.67660.7853-0.01450.2026-0.00390.0041-0.4696-0.0643-0.67270.70760.27470.33941.24660.43350.471196.5064130.6918192.0113
615.22730.7629-0.59213.2672-3.74965.78030.52630.41950.19970.32910.08530.3045-0.5253-0.0743-0.61160.65620.16030.18390.98480.49340.748684.0639123.7051208.5357
624.06272.1866-3.43543.3328-2.08124.89910.2821-0.3302-0.2488-0.15-0.16270.03940.2506-0.096-0.11930.5052-0.1456-0.10491.2920.7790.88466.9434103.457230.1635
631.28341.6186-0.41772.3393-0.2790.3892-0.04120.00580.0547-0.2466-0.45450.6701-0.3062-0.44260.49570.72310.1497-0.73492.03440.02671.975231.9122103.0136231.1776
640.02380.02370.00180.24530.0560.01530.08010.1083-0.06090.0728-0.16330.2543-0.0336-0.03650.08321.06290.0905-0.30382.140.29061.31334.1519117.563204.605
650.04-0.0035-0.01770.0110.00240.01010.1849-0.21570.0774-0.1172-0.0957-0.0751-0.08410.0955-0.08921.81740.12370.88682.45080.1131.743630.6908143.6618200.5648
660.00670.0038-0.00150.00610.00020.00190.0169-0.0383-0.0653-0.0776-0.0291-0.0829-0.0198-0.0490.01221.9822-0.22810.91942.73620.14711.220643.4082163.4656199.8887
670.60680.41440.5062.6393-1.59782.24190.2077-0.13790.0520.07410.1010.21380.7832-0.4357-0.30871.5665-0.09730.27421.26630.31021.973382.984471.2381237.0173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1ELECTRON MICROSCOPY1C1 - 247
2ELECTRON MICROSCOPY2C248 - 343
3ELECTRON MICROSCOPY2E151 - 181
4ELECTRON MICROSCOPY3C344 - 558
5ELECTRON MICROSCOPY4E12 - 150
6ELECTRON MICROSCOPY5F1 - 183
7ELECTRON MICROSCOPY6F184 - 355
8ELECTRON MICROSCOPY7L1 - 103
9ELECTRON MICROSCOPY8L104 - 197
10ELECTRON MICROSCOPY9L198 - 296
11ELECTRON MICROSCOPY10L297 - 402
12ELECTRON MICROSCOPY11M1 - 103
13ELECTRON MICROSCOPY12M104 - 197
14ELECTRON MICROSCOPY13M198 - 296
15ELECTRON MICROSCOPY14M297 - 402
16ELECTRON MICROSCOPY15G12 - 342
17ELECTRON MICROSCOPY15S32 - 55
18ELECTRON MICROSCOPY16G343 - 701
19ELECTRON MICROSCOPY16S19 - 31
20ELECTRON MICROSCOPY17S56 - 246
21ELECTRON MICROSCOPY18S265 - 524
22ELECTRON MICROSCOPY19S542 - 627
23ELECTRON MICROSCOPY20S648 - 1033
24ELECTRON MICROSCOPY20S2001 - 2107
25ELECTRON MICROSCOPY21S1043 - 1215
26ELECTRON MICROSCOPY22S1216 - 1443
27ELECTRON MICROSCOPY23H12 - 386
28ELECTRON MICROSCOPY23A29 - 55
29ELECTRON MICROSCOPY24H387 - 610
30ELECTRON MICROSCOPY24A19 - 28
31ELECTRON MICROSCOPY25A56 - 248
32ELECTRON MICROSCOPY26A262 - 401
33ELECTRON MICROSCOPY26B811 - 827
34ELECTRON MICROSCOPY27A402 - 524
35ELECTRON MICROSCOPY28A648 - 1034
36ELECTRON MICROSCOPY29A1043 - 1215
37ELECTRON MICROSCOPY30A1216 - 1443
38ELECTRON MICROSCOPY31B7 - 369
39ELECTRON MICROSCOPY32B385 - 431
40ELECTRON MICROSCOPY32P446 - 500
41ELECTRON MICROSCOPY33B471 - 655
42ELECTRON MICROSCOPY34B656 - 749
43ELECTRON MICROSCOPY34P672 - 685
44ELECTRON MICROSCOPY35B750 - 783
45ELECTRON MICROSCOPY35B828 - 859
46ELECTRON MICROSCOPY35P823 - 881
47ELECTRON MICROSCOPY36P5 - 435
48ELECTRON MICROSCOPY37P501 - 659
49ELECTRON MICROSCOPY38P701 - 822
50ELECTRON MICROSCOPY39O7 - 369
51ELECTRON MICROSCOPY40O385 - 432
52ELECTRON MICROSCOPY40Q449 - 500
53ELECTRON MICROSCOPY41O471 - 655
54ELECTRON MICROSCOPY42O656 - 749
55ELECTRON MICROSCOPY42Q669 - 685
56ELECTRON MICROSCOPY43O750 - 859
57ELECTRON MICROSCOPY43Q823 - 881
58ELECTRON MICROSCOPY44Q5 - 435
59ELECTRON MICROSCOPY45Q501 - 668
60ELECTRON MICROSCOPY46Q701 - 822
61ELECTRON MICROSCOPY47U1 - 169
62ELECTRON MICROSCOPY48U170 - 305
63ELECTRON MICROSCOPY49U306 - 399
64ELECTRON MICROSCOPY50U408 - 476
65ELECTRON MICROSCOPY51U477 - 550
66ELECTRON MICROSCOPY52U575 - 684
67ELECTRON MICROSCOPY53U696 - 800
68ELECTRON MICROSCOPY54U801 - 934
69ELECTRON MICROSCOPY55U949 - 1039
70ELECTRON MICROSCOPY56U1040 - 1154
71ELECTRON MICROSCOPY57U1155 - 1280
72ELECTRON MICROSCOPY58V45 - 187
73ELECTRON MICROSCOPY59V188 - 254
74ELECTRON MICROSCOPY60V255 - 311
75ELECTRON MICROSCOPY61V337 - 465
76ELECTRON MICROSCOPY62V466 - 623
77ELECTRON MICROSCOPY63V624 - 841
78ELECTRON MICROSCOPY64V916 - 1145
79ELECTRON MICROSCOPY65V1150 - 1250
80ELECTRON MICROSCOPY66V1251 - 1376
81ELECTRON MICROSCOPY67X1 - 153

+
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