[English] 日本語
Yorodumi
- PDB-6z7v: Crystal structure of Mindy2 (C266A) in complex with Lys48 linked ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z7v
TitleCrystal structure of Mindy2 (C266A) in complex with Lys48 linked di-ubiquitin (K48-Ub2)
Components
  • Polyubiquitin-C
  • Ubiquitin carboxyl-terminal hydrolase MINDY-2
KeywordsHYDROLASE / CYSTEINE PROTEASE / ISOPEPTIDASE AND UBIQUITIN BINDING
Function / homology
Function and homology information


K11-linked polyubiquitin modification-dependent protein binding / K6-linked polyubiquitin modification-dependent protein binding / cysteine-type carboxypeptidase activity / K48-linked deubiquitinase activity / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / Regulation of pyruvate metabolism / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Maturation of protein E ...K11-linked polyubiquitin modification-dependent protein binding / K6-linked polyubiquitin modification-dependent protein binding / cysteine-type carboxypeptidase activity / K48-linked deubiquitinase activity / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / Regulation of pyruvate metabolism / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR2 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53
Similarity search - Function
MINDY deubiquitinase / MINDY deubiquitinase domain / MINDY deubiquitinase / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. ...MINDY deubiquitinase / MINDY deubiquitinase domain / MINDY deubiquitinase / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / Polyubiquitin-C / Ubiquitin carboxyl-terminal hydrolase MINDY-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsAbdul Rehman, S.A. / Lange, S.M. / Kulathu, Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_12016/6 United Kingdom
European Research Council (ERC)677623 United Kingdom
CitationJournal: Mol.Cell / Year: 2021
Title: Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2.
Authors: Abdul Rehman, S.A. / Armstrong, L.A. / Lange, S.M. / Kristariyanto, Y.A. / Grawert, T.W. / Knebel, A. / Svergun, D.I. / Kulathu, Y.
History
DepositionJun 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 3, 2021Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase MINDY-2
B: Ubiquitin carboxyl-terminal hydrolase MINDY-2
C: Polyubiquitin-C
D: Polyubiquitin-C
E: Polyubiquitin-C
F: Polyubiquitin-C
G: Polyubiquitin-C
H: Polyubiquitin-C
I: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,11416
Polymers122,3759
Non-polymers7397
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Mindy1 and Mindy2 both are structurally identical. The SAXS measurements for Mindy2-Lys48 linked di-ubiquitin complex show it to be a dimer which consists of one molecule of Mindy2 ...Evidence: SAXS, Mindy1 and Mindy2 both are structurally identical. The SAXS measurements for Mindy2-Lys48 linked di-ubiquitin complex show it to be a dimer which consists of one molecule of Mindy2 and one polymer of ubiquitin (the individual chain of ubiquitin are covalently linked and are considered as a single molecule). This observation from MIndy2-Lys48 linked di-ubiquitin can be extrapolated onto Mindy1-Lys48 linked di-ubiquitin complex. Moreover, the structure-based mutational studies have validated the complex observed in the crystal structure.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16100 Å2
ΔGint-13 kcal/mol
Surface area42810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.011, 117.597, 125.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase MINDY-2 / Deubiquitinating enzyme MINDY-2 / Protein FAM63B


Mass: 31168.389 Da / Num. of mol.: 2 / Mutation: C266A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MINDY2, FAM63B, KIAA1164 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NBR6, ubiquitinyl hydrolase 1
#2: Protein
Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 50 mM potassium phosphate monobasic, 14% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.65→47.79 Å / Num. obs: 40463 / % possible obs: 98.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 58.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.044 / Rrim(I) all: 0.094 / Net I/σ(I): 11.8 / Num. measured all: 176139 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.65-2.764.50.6412037245690.7040.3360.7282.199.6
9.55-47.793.80.02335999350.9990.0120.02643.395.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.19rc7_4070refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JKN, 1UBQ

5jkn

1ubq


Resolution: 2.65→47.79 Å / SU ML: 0.3616 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 2094 5.18 %RANDOM
Rwork0.2127 38315 --
obs0.2148 40409 98.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.59 Å2
Refinement stepCycle: LAST / Resolution: 2.65→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7919 0 43 38 8000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328092
X-RAY DIFFRACTIONf_angle_d0.581310993
X-RAY DIFFRACTIONf_chiral_restr0.04341305
X-RAY DIFFRACTIONf_plane_restr0.00471415
X-RAY DIFFRACTIONf_dihedral_angle_d5.25191104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.710.38411320.33322542X-RAY DIFFRACTION99.48
2.71-2.780.34581250.3032590X-RAY DIFFRACTION99.16
2.78-2.850.31321520.27972529X-RAY DIFFRACTION99
2.85-2.940.35011260.28222557X-RAY DIFFRACTION98.97
2.94-3.030.35931390.27762503X-RAY DIFFRACTION97.42
3.03-3.140.31411400.28122547X-RAY DIFFRACTION98.57
3.14-3.270.34271480.2672554X-RAY DIFFRACTION99.16
3.27-3.420.26891340.23462548X-RAY DIFFRACTION98.97
3.42-3.60.3011450.22282554X-RAY DIFFRACTION98.4
3.6-3.820.26571200.20052520X-RAY DIFFRACTION96.7
3.82-4.120.22681230.19212567X-RAY DIFFRACTION98.1
4.12-4.530.19011390.15672573X-RAY DIFFRACTION97.94
4.53-5.190.18551480.16552526X-RAY DIFFRACTION96.4
5.19-6.530.23661790.20622567X-RAY DIFFRACTION97.51
6.53-47.790.23391440.19642638X-RAY DIFFRACTION94.75
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)
15.917206753362.35624446905-1.519643662157.450854121751.208622356212.70433759493-0.03918654224880.04847109346741.137138228480.382911832724-0.03575050183230.665611936817-1.12515300952-0.765787592180.03905944288230.8677869523390.301128431568-0.1400163856180.5824339433550.04738570837590.56709379399733.7571614344-44.994041185558.8588236728
21.48488817783-1.89451543168-0.8913337369934.7104857053-0.6927466992415.751675122640.203571662740.3823614232870.73164601863-0.183084679097-0.232747670371-0.549888458597-0.828521726408-0.1266398175480.03917119964940.513354582701-0.0900489616449-0.115632544780.5207397545720.09767973861290.61390841534246.2381756279-53.530365553747.3405482135
33.2833350387-1.8824217966-0.5889477657285.38091467183-0.4885091009554.98435342207-0.276314105641-0.08530881085680.1581933073090.4278476821940.13539935641-0.0619154201584-0.161935307637-0.5466829097430.1339217452420.353995608404-0.0396201117672-0.1247408568710.384196685395-0.01113949425720.30028849587840.6944094193-66.890363593863.6014192787
44.669312061691.42929158261-2.519501952428.76446357793.251234342935.448076257980.509374602366-0.507801220850.3364699852510.747005374762-0.572202023345-0.632639597272-0.5809220935010.3190657352020.05378367176760.70302368957-0.112030035878-0.2235303155360.4089718002580.034037247870.40040645409660.8013701236-62.877211896198.3718961374
58.566826189254.15666867142-2.119158193163.65842115408-1.608404947623.596599600930.441429257601-1.159569122690.9087806426991.24143670625-0.3885141181540.556868171196-0.728318941595-0.17536335601-0.01693873520491.0020734519-0.09404009231220.1190966805660.591903722017-0.04635305532060.53171246444347.0744820349-70.4064976308108.424693486
64.45194253973.088357473350.01110647314436.35689567321-0.8441149906992.50466387956-0.1473775703830.149403543588-0.029967597078-0.1579193621850.08498477629310.06404992276320.0404435229993-0.1586530864430.04798514448140.2930497195450.0591805265134-0.05508430802970.233705099064-0.03648291384120.28165127259848.6078663126-74.890696372583.6369223412
75.64776783565-0.9265341800852.327932160042.011326749074.877352812298.84779717532-0.130473518570.17771271452-0.7088935307490.784934406201-0.016662560899-1.449217463760.2733604309880.8279748897120.09732296244750.733153660721-0.0296176661630.02266213135030.3877745696290.07561152280410.91784994608556.8941032237-102.94342686892.7599449445
88.113758334274.182677473431.390142729759.55400182568-0.1273291349586.803903842960.135280368528-0.110753140832-0.5693596326680.349508189846-0.570746836011-0.6289230657030.2864381721710.3375201493460.4125708734640.5533710255610.0512226930760.03122978894690.2492949732340.01969977687530.55839064200552.9182646032-93.178114652594.4186059325
99.86384822515-2.604005853387.217753119534.02862910703-3.701408959342.003085305990.405360275599-0.60050813864-0.4579144376762.007812269570.2968177824670.8266991177490.358049757181-0.207136555766-0.7113789408651.316049195550.003732991365620.1029620870720.4094954139250.07149534466340.74589231088845.0433327925-101.81377433896.7581097285
102.42629183744-0.113715927715-0.4039987168631.9354203257-1.684955473622.75891816237-0.026527108539-0.346030791199-1.25536160662-0.586578635692-0.197160096919-0.4774313114810.886070418564-0.2450797530820.2164723597360.5874518268830.0037090871115-0.01783170105890.340159303473-0.03522797361240.89563306323249.1674819699-100.07427661992.183492874
117.357640874581.662225728652.625726407617.18252719470.3325599337114.02810341740.211702588949-0.0288659603763-0.1843554445980.1166152339920.0392517784990.7398085182360.505501144814-0.720499176225-0.2335873622040.854334333624-0.4985759090940.06072503835180.961327663283-0.05902874771820.51719539574128.4483668764-83.696561103640.2018676461
122.000668094681.599722371261.999486666839.69983981579-4.130611730652.00036385409-0.3312863530831.372847762060.0757794253781-2.770265262580.3892133081330.266477578214-0.391458213797-0.201652876496-0.05316130728521.29345208576-0.4682120225770.007905478710011.33709580954-0.03683174674780.56256783333731.5653476873-78.713757282926.3320204338
135.01544533927-1.923947051931.878434871872.012984732014.825167569136.20199989340.2349739090970.778715403311-0.131563262881-0.687672415471-0.6021040771190.8360852702370.0417886201976-1.142423687150.3454128454050.574734238542-0.147496314575-0.1186883030280.7043594003550.01762934595190.53745145733731.5817412627-72.720701074338.8493139987
142.0156719372.505115235973.276634244767.98447307897-4.433187407098.26672737543-0.5557846828591.09916539977-0.418620102105-1.482885346460.254887414301-0.3929523525781.036194405620.1318392319410.2774569726220.742744939275-0.1753365285750.19100250220.60240141751-0.1358212884640.58466374094939.8312284694-80.773656848632.2249527293
152.862795132411.524623745131.885500299331.001993965680.6078402155532.082165995790.01432877024710.321141490397-0.3451641428280.009560336840670.0298185024623-0.0663591189360.557555688676-0.507640170127-0.02060241987320.738455361565-0.382402555601-0.03956968663680.592470936918-0.07034262610450.42030402016835.9663758505-74.232166278545.5374639732
167.879707667882.19390671094-0.7177795082366.93759972356-3.711606705843.98094652695-0.247346030570.379907027847-0.658414093153-0.925710343576-0.208766949222-1.272161497890.5735294273941.023676362410.4325057988540.4329311004110.08457481236270.1228546201870.615943198141-0.03312817904350.62034952550271.1146413727-79.757007132375.0845394831
174.670238319070.623822172962-0.5426934007245.988042846460.9529076081037.408552939340.17092279197-0.0492583321103-0.1234781236610.151282353034-0.245479425585-1.032102096230.2933029092320.8040666375560.06563414336280.3712083522360.0897175988173-0.0495662129370.346500804006-0.01262530871940.62689204895666.5871975534-79.978779208282.741384616
182.007751234366.349017577912.675555068467.931703812589.187140934862.005647914830.140554053757-0.692329561807-1.217096564710.5967526774420.77156415765-1.04887671082-0.1182744699570.579685104082-0.9266602939420.505632927954-0.007303467537530.09623775189460.708158638821-0.09714994553190.5227479417970.6830816212-72.569554930982.8824701963
194.680210095050.3557509575590.8340353585480.193968122604-1.011147515377.014778637120.882977699376-0.2412233533710.2069832583510.890479898952-0.06618590758360.534860286379-0.0384329470944-2.11010044897-0.7783205064770.861299915482-0.1820833104880.4107521497650.7946999648830.03744885241561.1700849597324.6615764936-88.9107952388103.775563794
208.41776905486-7.20586158786-8.080607789562.002366567846.361175956522.00312194620.1032602027530.8109052334991.5250810865-0.604287800484-0.2076657935781.75475493997-1.1142930211-1.247516470720.09209473283990.6633849935720.132366635817-0.008393213487240.6110797806970.0207141415991.1942826086626.4790956774-84.915599461695.3403875526
212.00653073856-1.575708793283.841000810632.00865998899-8.898960947786.87135071053-0.173343623070.244188116252-0.7381643051650.914955594530.2329981868251.2072311916-0.864099595138-0.103999787379-0.03102761014850.6981992765520.04502876130040.1676196284650.737724917734-0.01032324381310.71668739129931.0576083665-79.318538801699.1175888798
227.98934985275-5.03823633546-1.014348779354.555221478634.319476272699.91310595879-0.325889154677-0.250685920598-0.6946055715120.9055363799780.3404341129080.6914040148090.307073705073-0.412662825329-0.003169943015960.700403710747-0.0817983613350.05452550050590.4005457672930.1138964710880.57795705298334.6279826123-93.1534744458102.062314366
236.625039492375.25525584844-7.21376877947.49551195332-3.523836894342.007542369910.456721480387-1.065979360390.2451760832461.85316352982-0.5446982074541.47865337763-0.4348029435520.04383773807960.08941783730270.886753572635-0.1044201753030.2525362610850.712143408258-0.03766183693730.64124919179931.7625015127-80.406129763105.153938955
245.51845170033-2.46364682169-6.275385788372.000743358474.618205925549.11707926642-0.8127631026810.132204187222-0.903798767286-0.311844848370.175763290517-0.07175416013270.6019367952540.6596386355530.6610934973570.617858626038-0.1167157679660.1755819875820.6357676735010.081057515360.85992527742263.7447550716-69.184171600532.7840220671
252.61823363915-1.79960514092-0.7188523480614.78885324135.023374361235.961895561630.1014352079320.3612018356760.1852671472590.2439335526270.206151302763-0.3607970206270.05520843351860.164671889739-0.2597580192820.621927781032-0.04617336490450.1746107826970.5555375054810.1572464271630.74224947939662.9929572768-70.547490604636.1777366232
268.44221831163-3.5310630311-2.855050258369.886726296196.932393865679.42160557472-0.3771709352330.792365279004-0.2958327118861.59754291612-0.144983858533-1.50908907960.03887301703690.795556581050.5115917804540.622229393768-0.210248154447-0.1170178794120.5445639997140.2345454642160.9799197389662.7628382035-70.48301829244.0324521721
276.48812227405-6.603958830897.388808216929.81488965569-4.987087403382.00478202433-0.458398935448-0.2568600399640.2127864225741.157559882160.114921337465-0.700880482973-1.158907862520.7598787819710.3654420481940.597347783774-0.217444806282-0.09597518437770.5952060413430.1240664457090.47989057736258.0834427435-63.8113553545.166582602
289.16378675166-0.725275408084-4.957497355342.001616862790.3367852647862.00081537619-0.09523612221550.2084861827490.337617959553-0.321490186689-0.4391834270330.632666324240.5286628039120.7146137815750.5245492631540.80274155658-0.05237859204490.03703144322870.42910445570.008102844851730.42287891583650.127516486-65.576670858833.7209624637
296.725932937961.97761826597-4.725485688557.6840827051-0.228104278965.43983754824-0.6589933445840.228267734837-0.0350586235983-0.8305440198710.1876873232920.2189550316530.4390823315470.2424454081220.4935154343070.686022466351-0.0242055551115-0.04381673625870.4142651683470.0594304737840.43293594232750.6615698831-73.994971046938.6076924775
309.14115353365-8.29420627967-8.802335077487.526096378847.95357762212.001731885290.04087755224631.33827228075-0.676947933149-1.213247834050.339010328192-1.362920339470.2988542622190.573242536977-0.3834164018070.7410623941850.01221637252530.1678302278140.758923626068-0.05346278539080.63725946095858.1730044118-74.180428429127.9371003511
312.01591434342-2.44012613366-7.930489858898.96005391563-1.760121591119.43007041371-0.167325177050.06483107593790.717655708474-0.2070740416240.257130363129-0.910552509351-0.9733840937080.764018469456-0.06840654755890.389904347862-0.114254567508-0.06486214642980.5331955453970.05313814802910.5344024684158.0769786975-60.966699076639.7732039847
329.95041248689-2.08236206162-1.524018149172.00679955899-2.769513474683.38896294653-0.440518739081-0.539594326184-1.138886017851.026128274650.3235293543181.06538379027-0.285253133797-1.426114653850.1077137116840.5798837763410.08960166239830.01425202459241.031757068210.1938312627710.64325784155320.9310112826-70.493402056669.9872915828
339.243309846463.87726414773-0.3376515251156.296483834381.097226308485.11751676226-0.0485236742995-0.105597353007-0.21650624173-0.0121737764373-0.2755842161291.7560295714-0.458352194262-2.690420782410.3279986791070.5428821919510.0614946976535-0.06625104515181.67631583550.0755240310330.97623361787314.1844750144-65.61413757765.2446849062
341.956667138161.5995551346-1.802656676179.081197591444.95807510336.97363963079-0.4950289759450.2635557284740.592601912248-0.6767712886290.1818459010741.04677932393-0.355456145579-1.287023866710.3123613391330.482855452840.108268309682-0.08330941221961.096298608270.147194747530.66521147224324.319189164-64.712657629258.1691568439
355.35979212449-4.67489243094-0.8163764842529.285073026061.476152054555.08519570999-0.3532654868940.0468502919529-0.5002869776040.05352208740420.5261831635870.974510735693-0.272339379092-0.531347808881-0.168173288420.365339014654-0.07377750476170.01190561202970.9400741578170.06968676143440.5251016113225.4184159391-68.153895426264.5614105894
360.01454679296860.208389997503-0.2279273043552.73943795816-3.028650793593.349718071650.1350105509860.4022753176130.01617321834-0.2344057437870.179355570311-0.111289415773-0.248405543678-0.55053655456-0.3055470228541.53444909623-0.1568389746540.3178684978652.117928959530.2667863126750.7218389759140.6962579165-43.563539530126.7292952426
375.44089483153-1.135692204880.8109511718825.27323569318-4.458372033167.50382475612-0.3593711782250.8090062014070.686355956092-0.6590970188870.618702635791-0.1437255037030.967824522803-1.99136477859-0.2297245563610.98546054539-0.09168821793260.09408757796481.403100409050.302644676841.0124707523440.9416877639-36.801144397129.1501109886
388.16639724351-3.30820269438-0.697374170722.88054642438-0.4224524261480.381858168290.7909535998951.476937073361.29235982317-0.356987026438-1.54113993836-0.5324603627690.6984583218860.05238125713850.7340703756021.00413011484-0.002018631283110.0273763985761.017889696530.2023156569830.62113791156141.4002480561-35.000867556138.0293217738
398.731011730315.30778311827-2.444223065268.41368717799-4.818130436948.101367640150.2583008190131.911885714321.38682352943-0.831392072738-0.213303874881-0.610609978453-1.32481893605-0.218692719352-0.0574660325991.039989117360.1661980841130.01180036696740.9581096009860.3056982378230.93502426941852.6000575226-39.14587271632.2141849378
408.495752063251.50862401251-7.704195011069.16401916402-1.737188397017.01670509880.4091460119650.962876342293-0.01008421184080.6409804831890.100293007773-0.08813056546850.173451866057-1.91800655075-0.5152488085720.871905945363-0.101692508432-0.1533202954121.30890288570.09393960645260.65729458079543.6890628721-42.351224389634.1823572071
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 240 through 288 )AA240 - 2881 - 49
22chain 'A' and (resid 289 through 360 )AA289 - 36050 - 121
33chain 'A' and (resid 361 through 499 )AA361 - 499122 - 260
44chain 'B' and (resid 241 through 288 )BB241 - 2881 - 48
55chain 'B' and (resid 289 through 334 )BB289 - 33449 - 94
66chain 'B' and (resid 335 through 499 )BB335 - 49995 - 259
77chain 'C' and (resid 1 through 34 )CC1 - 341 - 34
88chain 'C' and (resid 35 through 44 )CC35 - 4435 - 44
99chain 'C' and (resid 45 through 56 )CC45 - 5645 - 56
1010chain 'C' and (resid 57 through 76 )CC57 - 7657 - 76
1111chain 'D' and (resid 1 through 16 )DD1 - 161 - 16
1212chain 'D' and (resid 17 through 22 )DD17 - 2217 - 22
1313chain 'D' and (resid 23 through 44 )DD23 - 4423 - 44
1414chain 'D' and (resid 45 through 65 )DD45 - 6545 - 65
1515chain 'D' and (resid 66 through 76 )DD66 - 7666 - 76
1616chain 'E' and (resid 1 through 34 )EE1 - 341 - 34
1717chain 'E' and (resid 35 through 65 )EE35 - 6535 - 65
1818chain 'E' and (resid 66 through 73 )EE66 - 7366 - 73
1919chain 'F' and (resid 1 through 22 )FF1 - 221 - 22
2020chain 'F' and (resid 23 through 33 )FF23 - 3323 - 33
2121chain 'F' and (resid 34 through 44 )FF34 - 4434 - 44
2222chain 'F' and (resid 45 through 65 )FF45 - 6545 - 65
2323chain 'F' and (resid 66 through 73 )FF66 - 7366 - 73
2424chain 'G' and (resid 1 through 7 )GG1 - 71 - 7
2525chain 'G' and (resid 8 through 22 )GG8 - 228 - 22
2626chain 'G' and (resid 23 through 34 )GG23 - 3423 - 34
2727chain 'G' and (resid 35 through 44 )GG35 - 4435 - 44
2828chain 'G' and (resid 45 through 49 )GG45 - 4945 - 49
2929chain 'G' and (resid 50 through 59 )GG50 - 5950 - 59
3030chain 'G' and (resid 60 through 65 )GG60 - 6560 - 65
3131chain 'G' and (resid 66 through 73 )GG66 - 7366 - 73
3232chain 'H' and (resid 1 through 22 )HH1 - 221 - 22
3333chain 'H' and (resid 23 through 44 )HH23 - 4423 - 44
3434chain 'H' and (resid 45 through 55 )HH45 - 5545 - 55
3535chain 'H' and (resid 56 through 72 )HH56 - 7256 - 72
3636chain 'I' and (resid 1 through 7 )II1 - 71 - 7
3737chain 'I' and (resid 8 through 34 )II8 - 348 - 34
3838chain 'I' and (resid 35 through 44 )II35 - 4435 - 44
3939chain 'I' and (resid 45 through 59 )II45 - 5945 - 59
4040chain 'I' and (resid 60 through 74 )II60 - 7460 - 74

+
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://pdbjlvh1.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