[English] 日本語
Yorodumi
- PDB-7mph: GRB2 SH2 Domain with Compound 7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mph
TitleGRB2 SH2 Domain with Compound 7
ComponentsGrowth factor receptor-bound protein 2
KeywordsPROTEIN BINDING / Inhibitor / Complex / growth factor receptor / Ras-MAPK signaling cascade
Function / homology
Function and homology information


guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / MET activates PTPN11 / negative regulation of natural killer cell mediated cytotoxicity / MET activates RAP1 and RAC1 / vesicle membrane / Signaling by LTK / CD28 dependent Vav1 pathway / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / epidermal growth factor receptor binding / Regulation of KIT signaling / PI-3K cascade:FGFR3 / natural killer cell mediated cytotoxicity / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of actin filament polymerization / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / regulation of MAPK cascade / RET signaling / PI3K events in ERBB2 signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / insulin receptor substrate binding / signal transduction in response to DNA damage / SOS-mediated signalling / fibroblast growth factor receptor signaling pathway / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Role of LAT2/NTAL/LAB on calcium mobilization / SHC1 events in ERBB4 signaling / Interleukin receptor SHC signaling / RHO GTPases Activate WASPs and WAVEs / GAB1 signalosome / Signalling to RAS / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / ephrin receptor binding / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / Signaling by FGFR2 in disease / phosphotyrosine residue binding / myelination / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / FCERI mediated Ca+2 mobilization / NCAM signaling for neurite out-growth / GRB2 events in ERBB2 signaling / Downstream signal transduction / insulin-like growth factor receptor signaling pathway / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Constitutive Signaling by Overexpressed ERBB2 / T cell activation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to ionizing radiation / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of signaling by CBL / FCERI mediated MAPK activation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling
Similarity search - Function
GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Chem-ZLY / Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSun, L. / Schonbrunn, E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2021
Title: Synthesis and structural characterization of a monocarboxylic inhibitor for GRB2 SH2 domain.
Authors: Xiao, T. / Sun, L. / Zhang, M. / Li, Z. / Haura, E.B. / Schonbrunn, E. / Ji, H.
History
DepositionMay 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Growth factor receptor-bound protein 2
B: Growth factor receptor-bound protein 2
C: Growth factor receptor-bound protein 2
D: Growth factor receptor-bound protein 2
E: Growth factor receptor-bound protein 2
F: Growth factor receptor-bound protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,83136
Polymers66,0516
Non-polymers5,78030
Water2,000111
1
A: Growth factor receptor-bound protein 2
hetero molecules

F: Growth factor receptor-bound protein 2
hetero molecules

E: Growth factor receptor-bound protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,70616
Polymers33,0253
Non-polymers2,68113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area6600 Å2
ΔGint-69 kcal/mol
Surface area13970 Å2
MethodPISA
2
C: Growth factor receptor-bound protein 2
D: Growth factor receptor-bound protein 2
hetero molecules

B: Growth factor receptor-bound protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,12520
Polymers33,0253
Non-polymers3,09917
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area7020 Å2
ΔGint-111 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.885, 87.102, 136.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 59 through 70 or (resid 71...
21(chain B and (resid 59 through 68 or (resid 69...
31(chain C and (resid 59 through 66 or (resid 67...
41(chain D and (resid 59 through 66 or (resid 67...
51(chain E and (resid 59 through 71 or (resid 72...
61(chain F and (resid 59 through 66 or (resid 67...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALA(chain A and (resid 59 through 70 or (resid 71...AA59 - 702 - 13
12GLUGLUGLUGLU(chain A and (resid 59 through 70 or (resid 71...AA71 - 7214 - 15
13GLYGLYPHEPHE(chain A and (resid 59 through 70 or (resid 71...AA58 - 1471 - 90
14GLYGLYPHEPHE(chain A and (resid 59 through 70 or (resid 71...AA58 - 1471 - 90
15GLYGLYPHEPHE(chain A and (resid 59 through 70 or (resid 71...AA58 - 1471 - 90
16GLYGLYPHEPHE(chain A and (resid 59 through 70 or (resid 71...AA58 - 1471 - 90
21PROPROALAALA(chain B and (resid 59 through 68 or (resid 69...BB59 - 682 - 11
22LYSLYSGLUGLU(chain B and (resid 59 through 68 or (resid 69...BB69 - 7212 - 15
23GLYGLYILEILE(chain B and (resid 59 through 68 or (resid 69...BB58 - 1511 - 94
24GLYGLYILEILE(chain B and (resid 59 through 68 or (resid 69...BB58 - 1511 - 94
25GLYGLYILEILE(chain B and (resid 59 through 68 or (resid 69...BB58 - 1511 - 94
26GLYGLYILEILE(chain B and (resid 59 through 68 or (resid 69...BB58 - 1511 - 94
31PROPROPROPRO(chain C and (resid 59 through 66 or (resid 67...CC59 - 662 - 9
32ARGARGGLUGLU(chain C and (resid 59 through 66 or (resid 67...CC67 - 7210 - 15
33GLYGLYGLUGLU(chain C and (resid 59 through 66 or (resid 67...CC58 - 1521 - 95
34GLYGLYGLUGLU(chain C and (resid 59 through 66 or (resid 67...CC58 - 1521 - 95
35GLYGLYGLUGLU(chain C and (resid 59 through 66 or (resid 67...CC58 - 1521 - 95
36GLYGLYGLUGLU(chain C and (resid 59 through 66 or (resid 67...CC58 - 1521 - 95
41PROPROPROPRO(chain D and (resid 59 through 66 or (resid 67...DD59 - 662 - 9
42ARGARGGLUGLU(chain D and (resid 59 through 66 or (resid 67...DD67 - 7210 - 15
43GLYGLYGLUGLU(chain D and (resid 59 through 66 or (resid 67...DD58 - 1521 - 95
44GLYGLYGLUGLU(chain D and (resid 59 through 66 or (resid 67...DD58 - 1521 - 95
45GLYGLYGLUGLU(chain D and (resid 59 through 66 or (resid 67...DD58 - 1521 - 95
46GLYGLYGLUGLU(chain D and (resid 59 through 66 or (resid 67...DD58 - 1521 - 95
51PROPROGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE59 - 712 - 14
52GLUGLUGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE7215
53GLYGLYGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE58 - 1521 - 95
54GLYGLYGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE58 - 1521 - 95
55GLYGLYGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE58 - 1521 - 95
56GLYGLYGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE58 - 1521 - 95
61PROPROPROPRO(chain F and (resid 59 through 66 or (resid 67...FF59 - 662 - 9
62ARGARGGLUGLU(chain F and (resid 59 through 66 or (resid 67...FF67 - 7210 - 15
63PROPROGLUGLU(chain F and (resid 59 through 66 or (resid 67...FF59 - 1522 - 95
64PROPROGLUGLU(chain F and (resid 59 through 66 or (resid 67...FF59 - 1522 - 95
65PROPROGLUGLU(chain F and (resid 59 through 66 or (resid 67...FF59 - 1522 - 95
66PROPROGLUGLU(chain F and (resid 59 through 66 or (resid 67...FF59 - 1522 - 95

-
Components

#1: Protein
Growth factor receptor-bound protein 2 / Adapter protein GRB2 / Protein Ash / SH2/SH3 adapter GRB2


Mass: 11008.441 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB2, ASH / Production host: Escherichia coli (E. coli) / References: UniProt: P62993
#2: Chemical
ChemComp-ZLY / (4-{(10R,11E,14S,18S)-18-(2-amino-2-oxoethyl)-14-[(naphthalen-1-yl)methyl]-8,17,20-trioxo-7,16,19-triazaspiro[5.14]icos-11-en-10-yl}phenyl)acetic acid


Mass: 652.779 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H44N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12.4mg/mL GRB2 SH2 domain, 0.1mM Bis-Tris pH 5.5, 2M Ammonium Sulphate

-
Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→47.32 Å / Num. obs: 50672 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Net I/σ(I): 9.8 / Num. measured all: 336368 / Scaling rejects: 101
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
2-2.056.73.2892498437020.4451.3663.5650.6100
8.94-47.325.90.03238886590.9990.0140.03540.799.5

-
Processing

Software
NameVersionClassification
PHENIX1.18.2-3874_3874refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CJ1

1cj1


Resolution: 2→45.83 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 1996 3.95 %
Rwork0.2313 48501 -
obs0.2331 50497 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.38 Å2 / Biso mean: 66.3428 Å2 / Biso min: 37.39 Å2
Refinement stepCycle: final / Resolution: 2→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4471 0 394 111 4976
Biso mean--60.52 55.15 -
Num. residues----563
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2359X-RAY DIFFRACTION15.48TORSIONAL
12B2359X-RAY DIFFRACTION15.48TORSIONAL
13C2359X-RAY DIFFRACTION15.48TORSIONAL
14D2359X-RAY DIFFRACTION15.48TORSIONAL
15E2359X-RAY DIFFRACTION15.48TORSIONAL
16F2359X-RAY DIFFRACTION15.48TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.4731400.44453405354599
2.05-2.110.42221390.407633933532100
2.11-2.170.39161400.369734263566100
2.17-2.240.42451420.333434103552100
2.24-2.320.32281400.303234113551100
2.32-2.410.3731410.29334283569100
2.41-2.520.31531430.287934403583100
2.52-2.650.3461410.275534323573100
2.65-2.820.31021430.279134743617100
2.82-3.040.32281420.264934503592100
3.04-3.340.28311420.241634893631100
3.34-3.830.26481450.208735073652100
3.83-4.820.21951460.170935413687100
4.82-45.830.23511520.199336953847100
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)
17.82291.4789-2.64988.3047-1.88235.640.18980.49060.46861.04630.24081.0533-1.4345-1.7262-0.40590.90830.30640.17671.0031-0.02720.54587.72713.555731.8412
27.7037-0.35730.38180.0157-0.02340.0167-0.3153-2.07571.8770.6993-0.10991.2377-0.5895-1.24160.33812.050.6490.56531.0159-0.30851.05694.439125.730730.3674
34.6853-0.596-0.67695.6150.04716.6470.1319-0.02130.21660.39250.14970.174-0.7429-0.0208-0.27940.72920.04310.05160.3676-0.02820.374215.526415.076721.8936
44.5041-1.27115.18033.1271-2.9427.1761-0.4804-0.88451.55310.2363-0.3031-0.1772-3.0122-1.03440.72891.21470.0824-0.06480.6072-0.05050.631411.583525.946918.4371
57.8376-3.3557.068.3443-5.62137.5571-0.348-0.8106-0.2034-0.19260.74120.4792-1.26410.1708-0.37070.7311-0.1021-0.03620.66640.00520.381433.51743.193518.6046
68.1882-5.42440.53696.73230.25296.8501-0.2048-0.3638-1.03750.3776-0.17881.04041.2635-1.4160.41680.9187-0.36520.05050.952-0.05690.789524.775135.546716.3843
76.2628-4.2326-5.21225.68354.26678.52280.10960.3709-0.9904-0.4570.17770.242-0.16130.2195-0.29390.5961-0.0796-0.08630.59350.02030.472738.013642.647312.2481
88.83860.5409-2.36247.3884-2.77464.4692-0.4787-1.3737-0.70860.10180.22120.66270.8833-0.87620.18210.476-0.22050.04170.93450.02430.499926.858339.02948.1096
99.5909-0.1398-0.24113.974-0.37222.9759-0.0807-0.56080.05220.15070.02890.0544-0.1353-0.57130.09160.4608-0.0476-0.0040.5505-0.01530.324935.118952.44742.8335
109.61946.36193.71384.33042.80376.32860.2669-0.84132.02240.4362-0.3651.3839-1.0696-0.61770.08550.480.09380.04650.8316-0.08730.612426.535653.54449.4873
119.7034-0.0311-1.78339.47530.95075.4560.31070.15160.4551-0.0665-0.69110.8010.9332-1.31950.26270.4304-0.0932-0.11741.1068-0.00830.700420.454445.47916.1611
122.45350.39281.73018.41247.40897.5737-0.0835-0.1357-0.21740.0077-0.32160.11590.5395-0.76130.26850.7036-0.0473-0.1110.43320.00090.4955-5.024844.884411.6355
139.2276-4.0133-4.98863.21333.39053.76160.21410.53360.438-0.59010.5283-1.5672-0.15010.9474-0.87970.7045-0.0233-0.00350.72310.0040.55484.280943.87622.2042
144.90065.34233.9548.99630.3998.2603-0.3331-0.3294-1.42080.4967-0.3721-2.1710.89331.27960.58930.63940.1785-0.11550.79360.09430.80085.629832.36455.8418
156.8814-3.6454-1.60145.69056.47759.32840.0568-0.34860.3818-0.1810.10910.1154-0.4772-0.33160.02640.4768-0.0626-0.06910.31240.00610.4085-10.162444.77271.8629
166.14081.22020.98411.9672-0.03433.0415-0.2828-0.1831-0.3656-0.05250.1928-0.230.5345-0.02090.0920.61420.0383-0.03680.3953-0.03230.4106-10.872434.1227-1.5853
172.5834-3.67021.19136.295-4.23667.12280.0744-0.7971-1.2440.71820.11450.3350.9649-0.6029-0.23720.88980.0227-0.06660.51610.06640.5158-11.944429.75716.43
185.79761.26714.29891.69181.48273.5266-0.29931.5506-2.802-0.53610.6833-0.06882.83740.9524-0.29390.93650.0729-0.12370.6918-0.12830.733-3.621824.5714-1.9182
194.6988-0.4746-0.45681.83883.60557.5845-0.2882-0.7774-0.3772.4510.2558-1.48961.06921.0305-0.14611.19980.1761-0.30930.56770.09640.7199-0.073931.00758.8421
207.41121.30163.33213.75412.9933.16860.6983-0.2321-0.76650.64740.0142-0.19370.49410.1081-0.67290.6091-0.0076-0.09970.43450.07170.48150.727248.154813.9025
213.7496-0.49890.46781.37970.34563.38870.1701-0.4815-0.49120.1957-0.04960.10840.3998-0.4121-0.11930.5996-0.12130.01770.4572-0.00020.4128-11.736652.018520.3339
228.5172-0.9875-1.60398.41150.05886.25880.1634-0.47740.80470.07280.1138-0.0787-0.69770.2767-0.28460.4344-0.03770.06740.4163-0.04430.3791-7.143560.588715.5217
239.08275.765-0.64058.77440.1857.73240.984-0.3445-1.9504-1.1378-0.20730.5683-0.13880.6919-0.65470.60390.2619-0.00580.42160.03110.623243.488433.078844.2112
248.82-2.7448-3.46988.2333-1.9742.61680.2999-0.1446-1.43760.18890.021.09651.10170.4306-0.15552.59520.4632-0.51590.0780.14530.699140.574224.284136.636
253.91772.4493-5.94689.4734-5.69249.9662-0.95250.6727-1.8157-1.1045-0.0350.4260.4637-2.35620.85361.4184-0.4-0.32630.89840.0761.100430.087226.68238.7569
269.0703-1.25723.21673.74692.60483.88440.310.98590.2791-1.21480.5093-1.12390.76281.2141-0.8080.8674-0.00550.11460.77230.12590.796244.646238.93634.7567
277.43685.67571.65745.972.71781.53320.597-0.0617-1.2776-1.97310.02640.29952.0884-1.0073-0.38831.5368-0.4273-0.44370.65380.11440.813434.371734.251431.8347
287.0049-5.3109-0.37934.58060.78176.87510.31160.21440.2804-0.85020.26940.4097-0.6498-1.1887-0.56130.6752-0.0178-0.07070.52490.1330.464635.282850.697834.5886
298.4965.91283.46165.0644.80637.560.3148-1.6956-0.14531.41650.44492.12250.872-1.4352-0.70.6301-0.06790.03350.73230.33990.871830.73844.008441.6622
305.8726-4.37050.50587.3039-2.45916.38850.7899-0.3866-2.34690.01010.10952.49331.2071-1.1197-0.76530.5799-0.2289-0.22120.72340.20151.229726.019636.086836.9339
317.00881.79892.22677.452-4.23144.00740.29610.0243-0.3271.9589-0.0373-0.3067-1.2095-0.7642-0.28440.76450.0191-0.02380.4809-0.16680.59619.86977.205825.1896
325.30162.2532.12593.7567-2.38874.73691.02870.6338-1.1083-0.19590.7371-0.49211.09390.5818-1.50620.71970.0257-0.01620.5584-0.10790.705619.837267.379316.4056
339.01225.1457-4.51848.083-4.03368.08740.29420.54470.1050.9291-0.1296-0.3169-0.47-0.0515-0.11860.3792-0.05610.01590.34010.0170.307812.412171.496618.979
341.5912.04162.29487.95213.53288.0898-0.43190.4222-0.1555-0.65590.4405-1.2737-0.98570.8130.04550.437700.05960.4073-0.00480.540615.523779.540914.1468
353.537-1.9556-1.08727.5080.86124.25360.0539-0.12310.09850.642-0.11980.4862-0.0972-0.50160.10570.4934-0.07640.04820.5007-0.02110.37045.342481.715814.609
369.0903-0.86985.099.913-3.67253.90840.330.14020.2086-0.04610.07180.43590.706-0.0976-0.46320.5918-0.1080.09530.5175-0.03750.50443.017170.469916.5853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 75 )A58 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 82 )A76 - 82
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 137 )A83 - 137
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 148 )A138 - 148
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 66 )B58 - 66
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 82 )B67 - 82
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 94 )B83 - 94
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 109 )B95 - 109
9X-RAY DIFFRACTION9chain 'B' and (resid 110 through 127 )B110 - 127
10X-RAY DIFFRACTION10chain 'B' and (resid 128 through 137 )B128 - 137
11X-RAY DIFFRACTION11chain 'B' and (resid 138 through 151 )B138 - 151
12X-RAY DIFFRACTION12chain 'C' and (resid 58 through 66 )C58 - 66
13X-RAY DIFFRACTION13chain 'C' and (resid 67 through 75 )C67 - 75
14X-RAY DIFFRACTION14chain 'C' and (resid 76 through 82 )C76 - 82
15X-RAY DIFFRACTION15chain 'C' and (resid 83 through 94 )C83 - 94
16X-RAY DIFFRACTION16chain 'C' and (resid 95 through 127 )C95 - 127
17X-RAY DIFFRACTION17chain 'C' and (resid 128 through 136 )C128 - 136
18X-RAY DIFFRACTION18chain 'C' and (resid 137 through 146 )C137 - 146
19X-RAY DIFFRACTION19chain 'C' and (resid 147 through 152 )C147 - 152
20X-RAY DIFFRACTION20chain 'D' and (resid 58 through 82 )D58 - 82
21X-RAY DIFFRACTION21chain 'D' and (resid 83 through 127 )D83 - 127
22X-RAY DIFFRACTION22chain 'D' and (resid 128 through 152 )D128 - 152
23X-RAY DIFFRACTION23chain 'E' and (resid 58 through 67 )E58 - 67
24X-RAY DIFFRACTION24chain 'E' and (resid 68 through 73 )E68 - 73
25X-RAY DIFFRACTION25chain 'E' and (resid 74 through 82 )E74 - 82
26X-RAY DIFFRACTION26chain 'E' and (resid 83 through 94 )E83 - 94
27X-RAY DIFFRACTION27chain 'E' and (resid 95 through 110 )E95 - 110
28X-RAY DIFFRACTION28chain 'E' and (resid 111 through 127 )E111 - 127
29X-RAY DIFFRACTION29chain 'E' and (resid 128 through 136 )E128 - 136
30X-RAY DIFFRACTION30chain 'E' and (resid 137 through 152 )E137 - 152
31X-RAY DIFFRACTION31chain 'F' and (resid 59 through 66 )F59 - 66
32X-RAY DIFFRACTION32chain 'F' and (resid 67 through 76 )F67 - 76
33X-RAY DIFFRACTION33chain 'F' and (resid 77 through 87 )F77 - 87
34X-RAY DIFFRACTION34chain 'F' and (resid 88 through 101 )F88 - 101
35X-RAY DIFFRACTION35chain 'F' and (resid 102 through 137 )F102 - 137
36X-RAY DIFFRACTION36chain 'F' and (resid 138 through 152 )F138 - 152

+
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