[English] 日本語
Yorodumi
- PDB-9axx: Crystal structure of BRAF/MEK1 complex with NST-628 and an active... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9axx
TitleCrystal structure of BRAF/MEK1 complex with NST-628 and an active RAF dimer
Components
  • Dual specificity mitogen-activated protein kinase kinase 1
  • Serine/threonine-protein kinase B-raf
KeywordsTRANSFERASE / Inhibitor / complex / SIGNALING PROTEIN
Function / homology
Function and homology information


epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / trehalose metabolism in response to stress / CD4-positive, alpha-beta T cell differentiation / placenta blood vessel development / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / regulation of axon regeneration / mitogen-activated protein kinase kinase / negative regulation of synaptic vesicle exocytosis / type B pancreatic cell proliferation ...epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / trehalose metabolism in response to stress / CD4-positive, alpha-beta T cell differentiation / placenta blood vessel development / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / regulation of axon regeneration / mitogen-activated protein kinase kinase / negative regulation of synaptic vesicle exocytosis / type B pancreatic cell proliferation / labyrinthine layer development / MAP-kinase scaffold activity / head morphogenesis / Signalling to p38 via RIT and RIN / cerebellar cortex formation / myeloid progenitor cell differentiation / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / endothelial cell apoptotic process / Signaling by MAP2K mutants / negative regulation of fibroblast migration / positive regulation of glucose transmembrane transport / establishment of protein localization to membrane / regulation of Golgi inheritance / trachea formation / mitogen-activated protein kinase kinase binding / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / positive regulation of axonogenesis / regulation of stress-activated MAPK cascade / Frs2-mediated activation / protein kinase activator activity / ERBB2-ERBB3 signaling pathway / stress fiber assembly / positive regulation of axon regeneration / face development / endodermal cell differentiation / MAPK3 (ERK1) activation / synaptic vesicle exocytosis / somatic stem cell population maintenance / Bergmann glial cell differentiation / MAP kinase kinase activity / thyroid gland development / Uptake and function of anthrax toxins / MAP kinase kinase kinase activity / Schwann cell development / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / keratinocyte differentiation / positive regulation of stress fiber assembly / response to cAMP / ERK1 and ERK2 cascade / myelination / cellular response to calcium ion / protein serine/threonine/tyrosine kinase activity / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / substrate adhesion-dependent cell spreading / cellular response to nerve growth factor stimulus / insulin-like growth factor receptor signaling pathway / thymus development / Signal transduction by L1 / long-term synaptic potentiation / cell motility / animal organ morphogenesis / Spry regulation of FGF signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / visual learning / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / positive regulation of protein serine/threonine kinase activity / response to peptide hormone / neuron differentiation / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / chemotaxis / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / cellular response to xenobiotic stimulus / late endosome / presynapse / cell body / positive regulation of peptidyl-serine phosphorylation / T cell differentiation in thymus / regulation of cell population proliferation / heart development / T cell receptor signaling pathway / scaffold protein binding / protein tyrosine kinase activity / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / early endosome / non-specific serine/threonine protein kinase
Similarity search - Function
Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, 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
: / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase B-raf / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsQuade, B. / Huang, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cancer Discov / Year: 2024
Title: The pan-RAF-MEK non degrading molecular glue NST-628 is a potent and brain penetrant inhibitor of the RAS-MAPK pathway with activity across diverse RAS- and RAF-driven cancers.
Authors: Meagan B Ryan / Bradley Quade / Natasha Schenk / Zhong Fang / Marshall Zingg / Steven E Cohen / Brooke M Swalm / Chun Li / Aysegul Ozen / Chaoyang Ye / Maria Stella Ritorto / Xin Huang / ...Authors: Meagan B Ryan / Bradley Quade / Natasha Schenk / Zhong Fang / Marshall Zingg / Steven E Cohen / Brooke M Swalm / Chun Li / Aysegul Ozen / Chaoyang Ye / Maria Stella Ritorto / Xin Huang / Arvin C Dar / Yongxin Han / Klaus P Hoeflich / Michael Hale / Margit Hagel /
Abstract: Alterations in the RAS-MAPK signaling cascade are common across multiple solid tumor types and is a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents ...Alterations in the RAS-MAPK signaling cascade are common across multiple solid tumor types and is a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents phosphorylation and activation of MEK by RAF, overcoming the limitations of traditional RAS-MAPK inhibitors and leading to deep durable inhibition of the pathway. Cellular, biochemical, and structural analysis of RAF-MEK complexes show that NST-628 engages all isoforms of RAFand prevents the formation of BRAF-CRAF heterodimers, a differentiated mechanism from all current RAF inhibitors. With a potent and durable inhibition of the RAF-MEK signaling complex as well as high intrinsic permeability into the brain, NST-628 demonstrates broad efficacy in cellular and patient-derived tumor models harboring diverse MAPK pathway alterations, including orthotopic intracranial models. Given its functional and pharmacokinetic mechanisms that are differentiated from previous therapies , NST-628 is positioned to make an impact clinically in an areas of unmet patient need.
History
DepositionMar 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dual specificity mitogen-activated protein kinase kinase 1
B: Serine/threonine-protein kinase B-raf
C: Dual specificity mitogen-activated protein kinase kinase 1
D: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,09023
Polymers132,7414
Non-polymers3,34919
Water5,657314
1
B: Serine/threonine-protein kinase B-raf
C: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules

A: Dual specificity mitogen-activated protein kinase kinase 1
D: Serine/threonine-protein kinase B-raf
hetero molecules


  • defined by author
  • 136 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)136,09023
Polymers132,7414
Non-polymers3,34919
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Unit cell
Length a, b, c (Å)72.213, 82.408, 121.552
Angle α, β, γ (deg.)90.000, 105.650, 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

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Dual specificity mitogen-activated protein kinase kinase 1 / MAP kinase kinase 1 / MAPKK 1 / MKK1 / ERK activator kinase 1 / MAPK/ERK kinase 1 / MEK 1


Mass: 34543.836 Da / Num. of mol.: 2 / Mutation: S218A S222A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Production host: Homo sapiens (human)
References: UniProt: Q02750, mitogen-activated protein kinase kinase
#2: Protein Serine/threonine-protein kinase B-raf / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1


Mass: 31826.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Production host: Homo sapiens (human)
References: UniProt: P15056, non-specific serine/threonine protein kinase

-
Non-polymers , 6 types, 333 molecules

#3: Chemical ChemComp-A1AHE / N-[3-fluoro-4-({7-[(3-fluoropyridin-2-yl)oxy]-4-methyl-2-oxo-2H-1-benzopyran-3-yl}methyl)pyridin-2-yl]-N'-methylsulfuric diamide


Mass: 488.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H18F2N4O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.24 M di-ammonium hydrogen phosphate pH 8.0, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 2.07→58.52 Å / Num. obs: 83556 / % possible obs: 99.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 39.54 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.6
Reflection shellResolution: 2.07→2.11 Å / Rmerge(I) obs: 0.709 / Num. unique obs: 2636

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→41.2 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 4072 4.92 %
Rwork0.213 78704 -
obs0.2147 82776 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.81 Å2
Refinement stepCycle: LAST / Resolution: 2.07→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8730 0 215 314 9259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039140
X-RAY DIFFRACTIONf_angle_d0.557412378
X-RAY DIFFRACTIONf_chiral_restr0.04351383
X-RAY DIFFRACTIONf_plane_restr0.00421560
X-RAY DIFFRACTIONf_dihedral_angle_d15.0273316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.10.37521560.30822636X-RAY DIFFRACTION98.34
2.1-2.120.33421240.29392706X-RAY DIFFRACTION98.2
2.12-2.150.30611420.2712685X-RAY DIFFRACTION98.85
2.15-2.180.30971240.26622673X-RAY DIFFRACTION98.14
2.18-2.210.29521560.27352674X-RAY DIFFRACTION99.12
2.21-2.240.31691370.29682702X-RAY DIFFRACTION98.2
2.24-2.270.34411530.34222639X-RAY DIFFRACTION97.28
2.27-2.310.3281480.27072661X-RAY DIFFRACTION98.6
2.31-2.340.31351410.25452695X-RAY DIFFRACTION97.83
2.34-2.390.31451400.2542700X-RAY DIFFRACTION99.34
2.39-2.430.29061180.26092707X-RAY DIFFRACTION98.3
2.43-2.480.30651300.25652711X-RAY DIFFRACTION99.82
2.48-2.530.31251320.25312712X-RAY DIFFRACTION98.82
2.53-2.580.30141280.2512718X-RAY DIFFRACTION98.68
2.58-2.640.26741490.2422697X-RAY DIFFRACTION99.75
2.64-2.710.26731430.242699X-RAY DIFFRACTION99.16
2.71-2.780.31271530.23582711X-RAY DIFFRACTION99.13
2.78-2.860.2681390.24062725X-RAY DIFFRACTION99.27
2.86-2.950.26791400.25172722X-RAY DIFFRACTION99.34
2.95-3.060.30991440.24462715X-RAY DIFFRACTION99.44
3.06-3.180.29991250.23412732X-RAY DIFFRACTION99.65
3.18-3.330.25451550.22642729X-RAY DIFFRACTION99.69
3.33-3.50.23891500.21742719X-RAY DIFFRACTION99.65
3.5-3.720.2281300.20442753X-RAY DIFFRACTION99.76
3.72-4.010.24271390.18792755X-RAY DIFFRACTION99.69
4.01-4.410.19551630.1562722X-RAY DIFFRACTION99.9
4.41-5.050.1751450.15782770X-RAY DIFFRACTION99.93
5.05-6.360.20981400.18782779X-RAY DIFFRACTION99.93
6.36-41.20.20191280.1772857X-RAY DIFFRACTION99.63
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.93075425555-2.179387332630.1241683790123.32555634110.3711013275821.283569773780.5877574592450.5169705185710.126228655985-0.592826504207-0.1558401406370.0241199221438-0.447179081685-0.392636966888-0.1658462090360.8710605107760.3766029190530.5169494761791.004126143680.638939258371.6914719833-5.8756451281124.7331147421-57.1122114655
22.7180592791-0.415518588921.808066453411.446951338820.7886916320412.07062601073-0.03508055578780.456836625621-0.0395260136250.1521550753910.349590917550.8868467000210.0391858792445-0.747953917226-0.345279061810.406614332637-0.0661234728614-0.08379770338240.948356794820.382251762830.872850165257-10.24207393693.1553323235-56.3640448697
30.473284901331-0.480381084340.7652852115182.49817280718-0.1920943720631.422520029470.5326056621810.5221116875390.9650447134430.6221096629210.3920559441271.01155847171-0.492167606715-1.058768356170.125345599580.5263317189860.1332146324370.4063892285140.6002954937470.2940974359851.10744156414-8.269350430977.8619856844-44.3206134632
43.460668160261.14606472131-0.6226393062252.04201547359-1.21296117592.199616374720.07330280739110.3593656210160.2175670241570.1631386748910.5326357395290.741555993493-0.0157863366279-0.353603751285-0.5154123206650.2832637617530.0569168106118-0.01503209506830.4593511171830.1776313688620.5685387008215.128591803917.08169035322-57.3825246167
51.857725569890.619445691095-0.1079887410631.06425233204-0.2216295298950.05969622459950.754028310470.1417893177530.9622945473620.6422581031810.2086018471280.827862604498-0.776451711681-0.259974376339-0.5290295159280.5371071235550.02541780804720.3186707416310.3716568301240.08898676929210.6309413605727.8590724849417.222602753-50.0116352686
65.561825663780.9757038247480.230472087081.68678362592-0.04835596136671.238344950740.784495912298-0.2320428363470.5335941815950.88689029471-0.32864198220.365409303124-0.4541762933050.121815762435-0.3838874535870.693874567699-0.1556224917440.1887225223660.387625914144-0.04930952345360.4710935396017.636215477985.87018430517-38.5568934443
71.339516157440.5309068398220.2529074363370.3626715656380.2226101236592.832589072320.532313443624-0.2205819856320.2389425447640.624189107287-0.3777080254330.270766826338-0.5722177036160.465475039546-0.1656232480030.546216352165-0.2247202011910.1297463398530.431860375319-0.07613566083430.35075548204221.85561636911.9509400151-45.4126715095
85.675037408333.05583030881.02554475169.812071630191.706884236916.653038139260.2248290969070.5591175631370.685305957194-0.06212119365280.1306421451330.938885718518-0.642764015591-0.125572078843-0.2762665479530.3216765644780.06392847537150.1609378644340.3609404428650.1329861852970.42138486569413.151888182319.2011468426-63.4925692991
98.605499993041.42460294048-1.028865816555.50978900587-0.8576498121927.55432541047-0.224210797755-1.26571513577-1.305212183760.306630793576-0.112964940707-0.8091147555080.5140097185190.4772012308790.3456487704850.3703656021040.0104678206005-0.08724875634790.5213989170490.1703394945420.667227549012-1.8557449210738.2812881635-22.9555560512
104.136409855131.637073695561.608615946712.142026418611.186575430825.727277281120.0821359021052-0.0753818698754-0.815890883125-0.218753787663-0.167512151836-0.6371364066831.172006532670.1243953862320.03008348913920.630453315817-0.04387826805880.0424101700380.4066440897910.04002352181630.509352546098-5.6838676936132.4947480349-30.0501580746
115.631390311051.3312668875-1.78844584922.76792570631-0.05557700278182.20643488609-0.0833093473649-0.2635032974430.1149032642410.0974299365053-0.05136721523320.1406380334090.161417246147-0.02809589560770.1192467960870.360230643153-0.125527484348-0.03383374208680.308272994336-0.01620238216390.292618910098-19.114107458243.0557529415-29.1704958999
124.673616165851.784095664350.4108682628736.24759936892-3.608744508372.59000192685-0.09123414437960.421188099551-0.4467476833460.416985791912-0.4135361967540.3833544347131.19368093645-0.1711286258320.431253420360.371594866781-0.1547441262860.0438887581480.416776644405-0.06052129863940.397285616516-17.794048724333.5730620186-36.884986143
132.6166027892.047902172640.07777110159073.094108018480.07791399202521.47196830196-0.2818932554790.2786609753060.12082412302-0.1040361380050.2638816439060.0800052384090.508557002423-0.2842554503820.02820421483550.479843255269-0.259688312526-0.01522547706910.506198834968-0.05519219113840.405109302043-32.347220617229.7237223438-32.4915100359
142.130109100011.44955711422-0.1302459620782.911905419350.09661966982191.89577780752-0.4370917876760.5994953725930.589841769938-0.5655178453440.2039906739591.049911400660.158488094807-0.5441064537560.2241672892670.388767350318-0.221974262138-0.1535065873180.6660793739910.01733439047990.702520031291-39.222170990837.607554161-36.7502845862
151.584024530910.101966212606-1.511059557561.583104416361.342838415674.550577980940.07156279612780.01993576833070.804044767751-0.42163116759-0.4608778768920.852783226334-0.925274901782-0.3354502125930.4900470172650.671461967206-0.348965290612-0.3346791667950.7173250076470.09382688741440.836303213051-32.49399488351.3456007052-40.8781854225
164.419315517770.927179262841-1.371610310341.727771134870.528217745160.863618279348-0.520334515681-1.25825126333-0.3790360991940.575550484357-0.0556534179354-0.4993170392330.7083529639820.0418345616060.2964700153021.80542128059-0.227727165677-0.3838161345111.267788256680.2387299285950.676609153388-27.8290037824.422005771726.61371781775
176.00160246826-1.3725471312-1.629283308083.88241584871-0.1379664286595.271845643060.245894634242-0.5135576527670.4506855769240.5813550000820.564737714272-1.229414683840.02205998545221.07606924063-0.6828935341430.80284080523-0.123148122123-0.3585901200250.648061896322-0.02069048518670.885424686286-14.768576813719.0597155768-2.50168999486
182.212243075840.00432106586964-0.1853310411454.01864534399-0.5680207880882.083322886330.415490021909-0.541133071169-0.3359019205920.955745328884-0.266954754439-0.5846102790130.778484434709-0.0901686700769-0.1133328932861.11805735563-0.290187005982-0.2187434694130.5878653847650.06545938968390.47776668672-27.929598166112.7626328396-8.17334697437
190.408890008512-0.08617816617630.7127441408485.460137738133.565786373545.45950628280.0490691677179-0.1483840010810.1009258131110.2730572180170.079926858018-0.07772013028780.385610388158-0.19183573036-0.1563360002380.666294416949-0.3388178265070.03615372920720.587584879358-0.02186013247440.382224164833-35.1009062817.9020717029-19.58577612
202.325413228760.9386836397780.08754285234661.32795414913-0.8637553223961.1054449208-0.05370510358890.310790792958-0.50397305950.1735509473470.12624173784-0.4355039097630.933319614505-0.271407314216-0.0581718729621.01704810938-0.3537386881180.02576607331920.471381431042-0.0983183143880.509531670634-32.98488864667.03870032848-27.3967076372
211.115079462280.24075634168-0.1947982448980.7563316060890.5802568674320.877880206762-0.0314206972946-0.176905472371-0.7906895766430.907405913083-0.0311081495283-0.3470622195171.35645245308-0.1484566049080.1417061057691.67928020183-0.511501515761-0.08133296421080.5055434763630.0423334053450.729896560423-36.3817579593-4.631609812-18.2551670793
227.97301400910.0876841739922-1.1319809152.12241500003-1.141619186882.18159974560.1182379070630.5341165403490.356314838069-0.3953160686880.09153021786610.0603559996920.107600148861-0.481443406273-0.212135488320.345541885424-0.0688151636935-0.009615458811250.428170504089-0.006159607293850.265510483432-7.32972431511-23.6409666822-47.3407248926
232.481487754491.15825569511-0.7876493086593.80024211990.9152433598942.12517313610.183836143877-0.1023883852910.1001968568060.223345377812-0.1177187587520.165373776388-0.121632471405-0.170537338679-0.05984887669740.259239124687-0.09641522119350.02190624460510.360794294160.02160062195670.326700918086-6.64928409429-22.1111434946-31.2336484162
241.109695472591.26370019497-0.2891807224013.238440166390.1034719410132.346249891770.398032640825-0.4243579177710.03292966244660.485061567269-0.294011170454-0.202044294363-0.3918786982420.3705065857-0.1023730424450.391165464506-0.209873425044-0.0372071320350.47313607580.001099374542170.3227902868477.47583609378-14.9028259566-29.4141409924
255.17883114907-1.390796163012.898771878438.882212739880.6820113669711.872270396380.285244300177-1.47585590177-0.05756130416661.62065003722-0.305739918004-0.05087643233070.3586757113930.35525314166-0.006061832975810.637505108732-0.309189490376-0.1187955219190.7222184749580.1038123535140.409340372633.46161529839-25.2098412285-14.7695219616
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 41:59)AA41 - 591 - 19
22(chain A and resseq 60:92)AA60 - 9220 - 52
33(chain A and resseq 93:137)AA93 - 13753 - 97
44(chain A and resseq 138:162)AA138 - 16298 - 122
55(chain A and resseq 163:206)AA163 - 206123 - 166
66(chain A and resseq 207:241)AA207 - 241167 - 201
77(chain A and resseq 242:358)AA242 - 358202 - 276
88(chain A and resseq 359:383)AA359 - 382277 - 300
99(chain B and resseq 449:475)BC449 - 4751 - 21
1010(chain B and resseq 476:507)BC476 - 50722 - 53
1111(chain B and resseq 508:587)BC508 - 58754 - 133
1212(chain B and resseq 588:614)BC588 - 614134 - 154
1313(chain B and resseq 615:670)BC615 - 670155 - 210
1414(chain B and resseq 671:706)BC671 - 706211 - 246
1515(chain B and resseq 707:722)BC707 - 721247 - 261
1616(chain C and resseq 41:59)CD41 - 595 - 23
1717(chain C and resseq 60:92)CD60 - 9224 - 55
1818(chain C and resseq 93:206)CD93 - 20656 - 169
1919(chain C and resseq 207:241)CD207 - 241170 - 204
2020(chain C and resseq 242:319)CD242 - 319205 - 240
2121(chain C and resseq 320:383)CD320 - 378241 - 299
2222(chain D and resseq 449:507)DF449 - 5071 - 59
2323(chain D and resseq 508:569)DF508 - 56960 - 121
2424(chain D and resseq 570:706)DF570 - 706122 - 258
2525(chain D and resseq 707:722)DF707 - 720259 - 272

+
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