[English] 日本語
Yorodumi
- PDB-8jyr: Crystal structure of anti-HER2 antibody H2Mab-119 in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jyr
TitleCrystal structure of anti-HER2 antibody H2Mab-119 in complex with HER2 domain I
Components
  • H2Mab-119 VH-CH1
  • H2Mab-119 light chain
  • Receptor tyrosine-protein kinase erbB-2
KeywordsIMMUNE SYSTEM / HER2 / antibody
Function / homology
Function and homology information


negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / neuromuscular junction development / positive regulation of Rho protein signal transduction / ERBB2 Activates PTK6 Signaling / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / enzyme-linked receptor protein signaling pathway / positive regulation of transcription by RNA polymerase I / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of cell adhesion / positive regulation of protein targeting to membrane / regulation of angiogenesis / coreceptor activity / Schwann cell development / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / myelination / Downregulation of ERBB2:ERBB3 signaling / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / neurogenesis / basal plasma membrane / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of translation / positive regulation of epithelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / neuromuscular junction / Signaling by ERBB2 ECD mutants / neuron differentiation / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / cellular response to growth factor stimulus / Downregulation of ERBB2 signaling / ruffle membrane / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / presynaptic membrane / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / positive regulation of MAPK cascade / early endosome / cell surface receptor signaling pathway / receptor complex / endosome membrane / intracellular signal transduction / apical plasma membrane / positive regulation of protein phosphorylation / protein heterodimerization activity / protein phosphorylation / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsArimori, T. / Takagi, J.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02416 Japan
Japan Agency for Medical Research and Development (AMED)20am0101075 Japan
CitationJournal: Structure / Year: 2024
Title: Locally misfolded HER2 expressed on cancer cells is a promising target for development of cancer-specific antibodies.
Authors: Arimori, T. / Mihara, E. / Suzuki, H. / Ohishi, T. / Tanaka, T. / Kaneko, M.K. / Takagi, J. / Kato, Y.
History
DepositionJul 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Receptor tyrosine-protein kinase erbB-2
H: H2Mab-119 VH-CH1
L: H2Mab-119 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7694
Polymers70,5483
Non-polymers2211
Water8,557475
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.979, 112.291, 60.537
Angle α, β, γ (deg.)90.000, 90.761, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Receptor tyrosine-protein kinase erbB-2 / Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / ...Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / Tyrosine kinase-type cell surface receptor HER2 / p185erbB2


Mass: 22726.814 Da / Num. of mol.: 1 / Fragment: domain I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB2, HER2, MLN19, NEU, NGL / Production host: Homo sapiens (human)
References: UniProt: P04626, receptor protein-tyrosine kinase
#2: Antibody H2Mab-119 VH-CH1


Mass: 23821.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody H2Mab-119 light chain


Mass: 23999.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium citrate pH5.5, 20% w/v PEG3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.69→48.65 Å / Num. obs: 79311 / % possible obs: 99.1 % / Redundancy: 3.52 % / Biso Wilson estimate: 26.84 Å2 / CC1/2: 0.997 / Rsym value: 0.066 / Net I/σ(I): 9.46
Reflection shellResolution: 1.69→1.8 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.35 / Num. unique obs: 12651 / CC1/2: 0.694 / Rsym value: 0.912 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→40.02 Å / SU ML: 0.2017 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5072
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 3965 5 %
Rwork0.1734 75325 -
obs0.1752 79290 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.2 Å2
Refinement stepCycle: LAST / Resolution: 1.69→40.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4743 0 14 475 5232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01464861
X-RAY DIFFRACTIONf_angle_d1.32416608
X-RAY DIFFRACTIONf_chiral_restr0.0907747
X-RAY DIFFRACTIONf_plane_restr0.0111851
X-RAY DIFFRACTIONf_dihedral_angle_d6.378664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.710.36731290.35682457X-RAY DIFFRACTION91.44
1.71-1.740.35441440.33452734X-RAY DIFFRACTION99.62
1.74-1.760.32261410.31062668X-RAY DIFFRACTION99.57
1.76-1.780.34971430.29632722X-RAY DIFFRACTION99.65
1.78-1.810.3181410.27992679X-RAY DIFFRACTION99.82
1.81-1.830.35571430.28312720X-RAY DIFFRACTION99.79
1.83-1.860.32941430.26142707X-RAY DIFFRACTION99.89
1.86-1.890.28321420.24172695X-RAY DIFFRACTION99.89
1.89-1.930.26841420.21692700X-RAY DIFFRACTION99.68
1.93-1.960.21221420.19182696X-RAY DIFFRACTION99.82
1.96-20.26431430.19632709X-RAY DIFFRACTION99.55
2-2.040.2271410.18782682X-RAY DIFFRACTION99.65
2.04-2.080.23931420.18892702X-RAY DIFFRACTION99.23
2.08-2.130.23491410.17692682X-RAY DIFFRACTION99.54
2.13-2.190.231420.17612699X-RAY DIFFRACTION99.34
2.19-2.250.22661420.17772695X-RAY DIFFRACTION98.99
2.25-2.310.21981410.16632668X-RAY DIFFRACTION98.8
2.31-2.390.20091410.17332689X-RAY DIFFRACTION99.19
2.39-2.470.23811420.17832698X-RAY DIFFRACTION99.47
2.47-2.570.22951420.18212693X-RAY DIFFRACTION99.26
2.57-2.690.24011420.18412704X-RAY DIFFRACTION99.41
2.69-2.830.20941430.18372715X-RAY DIFFRACTION99.31
2.83-3.010.22471420.19022699X-RAY DIFFRACTION99.27
3.01-3.240.22121410.18382676X-RAY DIFFRACTION99.02
3.24-3.560.21391420.16792700X-RAY DIFFRACTION98.51
3.56-4.080.16631420.14132694X-RAY DIFFRACTION98.78
4.08-5.140.12411420.11692702X-RAY DIFFRACTION98.78
5.14-40.020.18011440.14742740X-RAY DIFFRACTION98.7
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)
13.46846502152.29462601876-0.405811716795.76664115369-1.022559210091.21469501767-0.1155305469640.270772186662-0.406072918771-0.03858450933330.170905443019-0.694794817905-0.3430535183870.362877545116-0.1490841948150.236351735969-0.03968101881770.0262197624020.26632224384-0.0940805890020.3700184497921.833290704139.5714484247-18.425848958
22.853535089930.02739654318020.4178661480215.510700395510.6082676612732.12365540566-0.02883978849570.0487935426971-0.1315405988160.1055680199550.149414984659-0.356463038951-0.1266822265540.121048365467-0.1213440726650.201524124717-0.009601653068480.009002714543420.218382195835-0.02476323912750.21967365297111.75902735433.3108445133-16.4439109027
35.4073576548-0.897527611691-0.1024611403478.007537246170.7518036105515.04265923779-0.2899568289970.444330866193-0.369132831943-0.3740767720260.315903514513-0.223434202436-0.1413455856280.0203205446987-0.02281530127850.244938725202-0.0687783711870.04332852309070.217869861254-0.05724302044150.18755198394911.103614030631.5701398596-24.6148189797
43.064108128861.89457456362-0.229250612172.799551280370.307380300140.367903895922-0.165814269080.245145862169-0.0972465088112-0.391711146650.228498519575-0.263988416981-0.03616053897090.12084337108-0.07285859296540.250057790806-0.0300286554780.009442135477070.211870733569-0.02838371321840.19543045385715.642182158139.9461265888-18.6260207984
53.442436464661.163152346960.03131337623677.602569290955.03526017889.23092170679-0.118527057125-0.5643758270060.1990138213510.009463294633710.141988058142-0.40107564934-0.3731264534530.3385822944870.07305550055750.1946401816890.0556116765617-0.04256259514130.349573840105-0.03821749625040.31508366551933.130378294467.111950043-6.45385685672
65.175282446280.2617633013860.2987619675544.131888851681.247540956972.90219761988-0.244697971257-0.530297220791-0.3628414229110.2956517268310.158866598737-0.2507393995550.394523263885-0.04190775069180.1006846106190.2911520286030.0246794283230.04195565252980.2849260116870.03508328563080.30256289165929.284326436556.3272317664-7.19032394641
75.979602592021.516740811390.6021888835716.1474203423.140256997221.63139004715-0.3275233569620.02564146180690.00765567505386-0.712182650540.19411387041-0.0817681454497-0.736094428686-0.5635837872710.1745500655530.187231019160.01420096017020.003572352002260.2074393248960.02725066641920.24194667194527.28962686861.9933758123-13.764622207
84.623456878871.477162381610.8450679823395.349792502943.774039281436.95063263292-0.186364014028-0.5893905494160.04543287830430.2554821813950.127292885708-0.3769831804030.1532147517540.5135157931870.3766488436080.2675451634120.0562687094402-0.03935176313910.405606972188-0.03280491800050.45489309200538.825779296161.2942735751-5.19198357096
95.088699104184.691585552885.010219716777.165930741355.589267314.933019580450.0122279337634-0.04485220058540.20912475084-0.169293369647-0.09763115647290.438818376648-0.256909504442-0.2038622505030.1198176794530.274168181110.0233869772716-0.004560112692290.189543761920.008938140576040.292338978604-3.6524196635852.4344666206-6.24396826985
102.711769003890.828998521674-0.04420290669463.288241560370.8284309344313.116298456230.07563473612-0.1244946807740.1158970354470.0725425471377-0.08502830297970.12346043117-0.00156597549263-0.05635550215330.00968929648210.2092566666540.01371600922220.00511222303260.1726919217580.006284181251690.204920782052-0.01627172439740.5031614691-7.95334345609
112.507686650510.6746780318080.3964587936324.642471167331.432117668544.575843812560.0575356121237-0.192767053747-0.03291639531410.32966128315-0.03014494898520.1377413736760.0456420618948-0.2048533060550.05287990113830.242232121929-0.0206950737020.04361764297790.195367428958-0.00463560303840.231826787106-3.1738104329242.0714248371-0.379544024638
120.5183599406331.261343833160.4649465988733.602578388041.86788698451.08468692069-0.0556181356282-0.03535106162440.0344939892769-0.1370381536210.003537456798920.14089341352-0.0470857937929-0.001770692669040.03328694314770.2343208446410.015106381875-0.009463116914270.2634148795820.001646338123630.2672182922823.5677378004650.7478653128-5.75277254232
136.589101053940.819081604549-4.316800243880.883930150239-0.6732014989884.134551689820.01064113852940.1566641495990.407402508143-0.1124316441670.205656880691-0.0332526892983-0.112131875319-0.0892523858421-0.2288462327560.239383831163-0.007597882309540.000676718539690.243393576763-0.0137834460580.29461210358725.760436711373.8964599947-10.9328907459
147.683117773764.90253626294-5.672766260525.98616207131-3.237635073124.21098541846-0.4142668639140.4496482310140.0913720999211-0.3886064055840.3987537535650.06116943805330.346767228883-0.4184634295070.02477135001410.226780563529-0.0152522623748-0.03583420517680.304349180262-0.01391596691860.25210692546517.104257230464.7686068869-7.71812748383
154.526081043410.693742403028-2.194289271072.96105803213-0.2700502011351.895982153460.2928574693620.2678200222410.765297213344-0.4312295266820.152412379745-0.283479833793-0.400206754695-0.00191158682957-0.4193084061410.348959740323-0.001099170236470.1016784420590.2764672531910.01641519420940.43608576058126.562519136679.0948740899-11.8629701187
162.895655791540.0222399270338-0.3020747704743.0748056596-0.1819836129192.74541175670.01773171069620.070547922078-0.274411585253-0.0436563862179-0.0009687843274210.1511486012060.468071639689-0.251238613543-0.004075359443510.314315162584-0.0596275945487-0.03705136910070.255484771586-0.006538896351610.228447597997-5.958844316692.76488846204-18.5020508927
176.630211158891.152579868320.1690157425167.06825749271.804291432075.702998741020.03285293967010.08077738613750.02424213190760.04540241878110.0502213540660.1433137409750.230447250914-0.253588395436-0.01163537448750.201237644655-0.02243966701870.004032918932250.178897599640.05402305397390.154904284535-5.0317310936714.0157952854-20.5535277042
186.325089805834.057989556514.285564454062.624177111072.680959189762.98629968045-0.2410354738010.488934053309-0.288580348076-0.5257854723480.0565197394342-0.3012913878870.9677710128270.630818849366-0.06284299431350.577025970725-0.03129712200080.1086731200830.34887966044-0.04656000851340.4135342324914.991969474843.46630702201-32.1206118474
191.97242218998-0.761184396551-1.31656599212.703036155371.576116641082.71005460442-0.02117875346850.162592195291-0.0304485030252-0.3301571388110.05448797682580.0558189766938-0.0977322657674-0.0990415600047-0.03836960788370.235694874857-0.0297135939393-0.03104994162760.2440424793350.0177815624730.225689881534-2.7918908908219.1900899996-27.355448617
203.49265129052-3.226804722622.844926626733.13446676905-2.427988138892.833738490850.3506282805670.640638230811-0.516355816518-0.639552455196-0.1105586240460.3066883180690.0510922190493-0.278888012519-0.1118718474530.4445930958580.00217528152994-0.02360686024520.454093209649-0.05810466463980.2746698155210.78164619224613.7349457903-41.1955088955
212.188006310971.306738667471.694067996292.08835013641.464681367045.249691115030.1695095846560.6387337695920.122516399234-0.385271511911-0.2010675836610.835349574988-0.0248390196905-0.5476709633320.05393437218510.502932852382-0.0629172856534-0.04445689719760.4874886482740.02112309123240.407828767246-9.0945943692417.2195351494-38.4638277478
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 17 )HC1 - 171 - 17
22chain 'H' and (resid 18 through 56 )HC18 - 5618 - 57
33chain 'H' and (resid 57 through 75 )HC57 - 7558 - 76
44chain 'H' and (resid 76 through 119 )HC76 - 11977 - 126
55chain 'H' and (resid 120 through 145 )HC120 - 145127 - 148
66chain 'H' and (resid 146 through 168 )HC146 - 168149 - 171
77chain 'H' and (resid 169 through 184 )HC169 - 184172 - 187
88chain 'H' and (resid 185 through 214 )HC185 - 214188 - 217
99chain 'L' and (resid 1 through 25 )LD1 - 251 - 25
1010chain 'L' and (resid 26 through 48 )LD26 - 4826 - 52
1111chain 'L' and (resid 49 through 75 )LD49 - 7553 - 79
1212chain 'L' and (resid 76 through 113 )LD76 - 11380 - 117
1313chain 'L' and (resid 114 through 155 )LD114 - 155118 - 159
1414chain 'L' and (resid 156 through 174 )LD156 - 174160 - 178
1515chain 'L' and (resid 175 through 211 )LD175 - 211179 - 215
1616chain 'A' and (resid 23 through 92 )AA23 - 921 - 70
1717chain 'A' and (resid 93 through 117 )AA93 - 11771 - 95
1818chain 'A' and (resid 118 through 138 )AA118 - 13896 - 105
1919chain 'A' and (resid 139 through 184 )AA139 - 184106 - 151
2020chain 'A' and (resid 185 through 199 )AA185 - 199152 - 166
2121chain 'A' and (resid 200 through 215 )AA200 - 215167 - 182

+
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