[English] 日本語
Yorodumi
- PDB-7tpb: p120RasGAP SH3 domain in complex with DLC1 RhoGAP domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tpb
Titlep120RasGAP SH3 domain in complex with DLC1 RhoGAP domain
Components
  • Ras GTPase-activating protein 1
  • Rho GTPase-activating protein 7
KeywordsSIGNALING PROTEIN / SH3 domain / RhoGAP domain / complex / GTPase
Function / homology
Function and homology information


negative regulation of Ras protein signal transduction / GTPase activator activity / positive regulation of GTPase activity / MAPK cascade
Similarity search - Function
Ras GTPase-activating protein 1 / RasGAP, SH3 domain / Ras GTPase-activating protein 1, C-terminal SH2 domain / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain ...Ras GTPase-activating protein 1 / RasGAP, SH3 domain / Ras GTPase-activating protein 1, C-terminal SH2 domain / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Rho GTPase activation protein / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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 / PH-like domain superfamily
Similarity search - Domain/homology
cDNA FLJ61389, highly similar to Ras GTPase-activating protein 1 / Isoform 6 of Rho GTPase-activating protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsStiegler, A.L. / Boggon, T.J. / Chau, J.E. / Vish, K.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R01NS117609 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138411 United States
CitationJournal: Nat Commun / Year: 2022
Title: SH3 domain regulation of RhoGAP activity: Crosstalk between p120RasGAP and DLC1 RhoGAP.
Authors: Chau, J.E. / Vish, K.J. / Boggon, T.J. / Stiegler, A.L.
History
DepositionJan 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 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: Ras GTPase-activating protein 1
B: Rho GTPase-activating protein 7
C: Ras GTPase-activating protein 1
D: Rho GTPase-activating protein 7
E: Ras GTPase-activating protein 1
F: Rho GTPase-activating protein 7
G: Ras GTPase-activating protein 1
H: Rho GTPase-activating protein 7


Theoretical massNumber of molelcules
Total (without water)134,6468
Polymers134,6468
Non-polymers00
Water0
1
A: Ras GTPase-activating protein 1
B: Rho GTPase-activating protein 7


Theoretical massNumber of molelcules
Total (without water)33,6622
Polymers33,6622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-6 kcal/mol
Surface area13020 Å2
MethodPISA
2
C: Ras GTPase-activating protein 1
D: Rho GTPase-activating protein 7


Theoretical massNumber of molelcules
Total (without water)33,6622
Polymers33,6622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-6 kcal/mol
Surface area13220 Å2
MethodPISA
3
E: Ras GTPase-activating protein 1
F: Rho GTPase-activating protein 7


Theoretical massNumber of molelcules
Total (without water)33,6622
Polymers33,6622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-7 kcal/mol
Surface area13060 Å2
MethodPISA
4
G: Ras GTPase-activating protein 1
H: Rho GTPase-activating protein 7


Theoretical massNumber of molelcules
Total (without water)33,6622
Polymers33,6622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-6 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.745, 143.745, 152.776
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 283 through 339)
21(chain C and resid 283 through 339)
31(chain E and resid 283 through 339)
41(chain G and resid 283 through 339)
12(chain B and (resid 1070 through 1088 or resid 1090...
22(chain D and (resid 1070 through 1088 or resid 1090...
32(chain F and (resid 1070 through 1088 or resid 1090...
42(chain H and (resid 1070 through 1088 or resid 1090...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGVALVAL(chain A and resid 283 through 339)AA283 - 3398 - 64
211ARGARGVALVAL(chain C and resid 283 through 339)CC283 - 3398 - 64
311ARGARGVALVAL(chain E and resid 283 through 339)EE283 - 3398 - 64
411ARGARGVALVAL(chain G and resid 283 through 339)GG283 - 3398 - 64
112TYRTYRGLYGLY(chain B and (resid 1070 through 1088 or resid 1090...BB1070 - 108815 - 33
122PROPROSERSER(chain B and (resid 1070 through 1088 or resid 1090...BB1090 - 112035 - 65
132ILEILEILEILE(chain B and (resid 1070 through 1088 or resid 1090...BB112267
142ALAALALEULEU(chain B and (resid 1070 through 1088 or resid 1090...BB1124 - 123969 - 184
152PROPROCYSCYS(chain B and (resid 1070 through 1088 or resid 1090...BB1258 - 1280203 - 225
212TYRTYRGLYGLY(chain D and (resid 1070 through 1088 or resid 1090...DD1070 - 108815 - 33
222PROPROSERSER(chain D and (resid 1070 through 1088 or resid 1090...DD1090 - 112035 - 65
232ILEILEILEILE(chain D and (resid 1070 through 1088 or resid 1090...DD112267
242ALAALACYSCYS(chain D and (resid 1070 through 1088 or resid 1090...DD1124 - 128069 - 225
312TYRTYRGLYGLY(chain F and (resid 1070 through 1088 or resid 1090...FF1070 - 108815 - 33
322PROPROSERSER(chain F and (resid 1070 through 1088 or resid 1090...FF1090 - 112035 - 65
332ILEILEILEILE(chain F and (resid 1070 through 1088 or resid 1090...FF112267
342ALAALACYSCYS(chain F and (resid 1070 through 1088 or resid 1090...FF1124 - 128069 - 225
412TYRTYRGLYGLY(chain H and (resid 1070 through 1088 or resid 1090...HH1070 - 108815 - 33
422PROPROSERSER(chain H and (resid 1070 through 1088 or resid 1090...HH1090 - 112035 - 65
432ILEILEILEILE(chain H and (resid 1070 through 1088 or resid 1090...HH112267
442ALAALACYSCYS(chain H and (resid 1070 through 1088 or resid 1090...HH1124 - 128069 - 225

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Ras GTPase-activating protein 1


Mass: 7622.630 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4DTL8
#2: Protein
Rho GTPase-activating protein 7 / Deleted in liver cancer 1 protein / DLC-1 / HP protein / Rho-type GTPase-activating protein 7 / ...Deleted in liver cancer 1 protein / DLC-1 / HP protein / Rho-type GTPase-activating protein 7 / START domain-containing protein 12 / StARD12 / StAR-related lipid transfer protein 12


Mass: 26038.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLC1, ARHGAP7, KIAA1723, STARD12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96QB1-6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M Magnesium nitrate, 16.5% PEG 3350 / Temp details: ambient temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 19702 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 80.44 Å2 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.09 / Rrim(I) all: 0.272 / Χ2: 1.055 / Net I/σ(I): 5.3 / Num. measured all: 179535
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.317.81.719520.3320.6571.8241.038100
3.31-3.458.61.07719960.6710.3911.1461.04100
3.45-3.68.90.79619570.8410.2820.8451.049100
3.6-3.799.90.53919800.9040.180.5691.0899.9
3.79-4.039.80.41419510.9550.1390.4371.084100
4.03-4.349.30.31519720.970.1090.3341.075100
4.34-4.788.40.23319770.9750.0850.2491.041100
4.78-5.478.60.19119770.9810.0690.2041.058100
5.47-6.8910.40.17719740.9910.0580.1861.02799.9
6.89-509.20.12219660.9920.0420.131.04899.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.8.2phasing
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
HKL-20002.3.8data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KUQ, 2J05
Resolution: 3.2→48.25 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 31.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 920 4.74 %
Rwork0.2125 18492 -
obs0.2149 19412 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.34 Å2 / Biso mean: 85.5158 Å2 / Biso min: 41.43 Å2
Refinement stepCycle: final / Resolution: 3.2→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8096 0 0 0 8096
Num. residues----1010
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A684X-RAY DIFFRACTION2.414TORSIONAL
12C684X-RAY DIFFRACTION2.414TORSIONAL
13E684X-RAY DIFFRACTION2.414TORSIONAL
14G684X-RAY DIFFRACTION2.414TORSIONAL
21B2252X-RAY DIFFRACTION2.414TORSIONAL
22D2252X-RAY DIFFRACTION2.414TORSIONAL
23F2252X-RAY DIFFRACTION2.414TORSIONAL
24H2252X-RAY DIFFRACTION2.414TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.2-3.370.33221220.300726582780
3.37-3.580.31871310.26726482779
3.58-3.860.27141250.233426332758
3.86-4.240.26431270.216426672794
4.24-4.860.26481270.185126342761
4.86-6.110.26041420.221626252767
6.12-48.250.21961460.177626272773
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)
15.67433.73772.12337.02672.93821.5412-1.74423.0903-0.0837-1.72231.0848-1.64880.07460.09170.30480.6417-0.331-0.02290.9805-0.49130.68447.834256.007297.62
24.2722-5.38860.17145.5810.59328.79890.1466-0.55650.20480.68150.79780.17740.41950.5618-0.8070.6811-0.1024-0.11960.63560.03960.71893.448559.5374102.3639
34.8944-1.4106-0.34743.76421.32572.9373-0.5342-1.0403-0.54290.21850.07980.18320.35240.40540.31730.6049-0.0128-0.10460.80380.02970.58584.464455.7971102.651
45.32880.2051-5.11589.59483.81598.33820.28880.74090.15331.1466-0.06040.6181-0.4654-0.0879-0.20090.6975-0.05870.00260.75950.15930.5032-30.081472.1401113.0788
56.8277-2.3767-1.34835.479-0.11485.3237-0.30020.31040.3869-0.45070.35720.38190.268-0.35920.07050.4468-0.0941-0.12580.6739-0.01740.3478-22.75165.421396.4412
62.28550.2387-3.05566.48642.89388.98690.00091.00940.3531-0.5245-0.09650.2092-1.56440.02790.20750.7798-0.1228-0.19390.75110.02980.4117-24.577269.030198.7736
75.1211-6.10082.34198.57770.07464.634-0.44250.1139-0.37641.12910.3785-0.76630.17110.25380.01810.6288-0.0797-0.15380.60350.07780.6158-11.449560.5357119.2074
81.95370.36042.17936.87760.90765.4059-1.16180.3177-3.11190.33650.86610.08480.4796-0.9801-0.25411.1922-0.0941-0.1520.6990.04670.7649-14.337149.2398121.1649
95.3419-0.67040.55064.63121.39652.67940.47530.1103-0.51660.0078-0.0862-0.20440.568-0.0501-0.26480.6725-0.1414-0.18670.38810.04060.3939-15.526357.9289106.5778
104.3543-3.47132.16933.2485-0.93262.97151.17290.4715-0.98622.0765-0.3775-0.91160.56090.9561-0.60860.6614-0.1343-0.19730.7263-0.00780.5014-7.753455.7112113.2531
115.79570.7196.02938.04251.21276.43890.4159-1.4282.25981.1216-1.22251.34951.2144-0.45020.85221.0075-0.17380.42760.98080.07531.1084-27.022772.061154.0928
123.7082-3.23372.66971.9487-2.47856.3118-0.2784-0.31031.05620.4171-0.04090.26510.1708-0.31580.32960.6827-0.02540.03770.4661-0.15810.9702-20.457870.846151.0509
139.047-2.4387-4.85763.04181.00286.28640.550.18130.7706-0.2047-0.60550.48241.4154-0.5215-0.05590.8528-0.0881-0.09840.64680.14020.5569-24.12569.2524150.8132
142.025-1.2972-1.17199.83273.90352.1248-0.4589-0.48151.1484-1.11480.0942-0.2963-0.9046-0.13180.24130.69160.1149-0.22080.8143-0.13350.825410.331452.95139.4324
157.8234-0.95480.64175.4091.52875.63750.07950.08850.06260.9182-0.1873-0.67770.61160.4030.04860.94250.0484-0.33760.45940.00640.59020.984954.1372156.3654
164.60932.5628-2.72495.77820.33014.1404-0.9346-1.32531.1733-1.18481.6831-1.87570.70160.8015-0.53091.39940.045-0.23310.8927-0.07520.470610.514450.9975156.3866
174.60731.1282-3.16966.51351.14859.48840.09180.56330.13340.4327-0.41170.2353-1.3449-0.09630.39670.8638-0.0084-0.29240.47920.02490.5486-0.389558.8576146.9388
184.9686-3.3082-2.24955.56590.74549.1244-0.0171.0797-0.3025-0.8382-0.02040.8440.457-0.0732-0.01381.0618-0.1085-0.39030.6480.15990.6919-17.079754.7927132.1116
194.59911.0548-0.13256.3465-2.23691.9070.34633.129-1.303-0.4146-1.35070.15523.22410.27760.38591.2418-0.5607-0.272-1.1832-0.27350.4289-7.899547.7746146.5027
203.0581-1.8826-3.24353.0953-1.30077.75540.7234-0.47920.42520.4412-0.2618-0.0742-0.1361-0.4805-0.1120.7486-0.1336-0.20770.5420.0050.7036-11.62562.1187146.395
219.2299-2.88981.58551.3446-1.93788.14660.0749-0.06230.1965-1.67380.44290.3756-0.3084-1.636-0.63251.23460.03-0.17650.57020.13890.5138-16.742457.9394140.3162
226.4337-0.6814-4.13023.4007-2.11874.1903-0.0906-1.79331.5089-0.4843-1.5133-1.65761.62162.7988-0.09190.5465-0.3155-0.34910.5928-0.58061.014926.680111.4661128.2253
236.2498-0.2327-0.37094.95681.24863.9312-0.06251.5695-2.004-0.26361.10820.6074-0.48930.9167-1.02820.6773-0.0855-0.04040.8154-0.12841.29320.235912.7378124.696
245.1181-5.4365-0.75495.46810.56776.34650.6131.0021-0.2734-0.1547-0.7249-0.64040.9790.00230.11480.7009-0.01210.07670.6266-0.15510.858423.786914.4224124.5332
253.6352.52261.67854.41491.22673.9143-0.32241.8153-0.8188-1.61170.17590.3815-0.10540.26360.1540.73570.10690.08040.66070.0860.6703-13.257925.1966115.6894
262.30170.20013.06924.1593-3.10556.95480.43071.16060.1714-0.9933-0.58080.6426-0.1294-0.21650.30831.0390.254-0.0811.1412-0.14440.5821-9.470733.4335112.1857
272.5792-0.12223.03775.22530.64345.07470.238-0.12870.9287-0.1493-0.31340.1556-0.8190.27680.27160.833-0.00230.07870.59240.0460.4255-2.781135.7189127.7499
282.1688-1.15011.89625.2501-0.88296.4421-0.477-0.9329-2.0618-0.38850.12370.03130.4318-0.102-0.03520.6380.0105-0.0460.5129-0.05980.1547-0.938824.3667131.95
294.7204-0.24892.56891.6998-3.04128.32490.15780.18540.1022-0.0968-0.12530.1247-0.3863-0.4898-0.00550.80780.12020.03890.3631-0.00090.438-4.084926.854124.1835
304.6601-2.3630.74512.1712-1.99413.2812-0.40932.9658-2.6945-0.98170.7589-1.24841.12312.180.59141.1582-0.00250.42931.4492-0.5440.982416.937424.4619105.78
317.3219-8.39517.02941.7337-5.61339.1801-1.17681.47511.77291.7957-0.292-3.3733-0.38130.0404-0.3981.4577-0.38290.28790.8755-0.20420.181816.113534.0412106.761
328.295-1.5025.77443.29340.32358.4264-0.3102-0.45350.7975-0.2699-0.5616-0.3298-1.1519-0.5740.63790.7483-0.15980.17320.5356-0.07620.54927.23835.7265120.9382
338.8972.58652.39522.7238-2.36767.8650.4803-0.5898-0.1638-0.2107-0.2857-0.9281-1.03320.1285-0.42910.45840.0217-0.0830.6762-0.04560.535111.151221.3784120.351
344.21872.15071.44256.83091.03137.8274-0.25640.4357-1.3219-1.45171.8565-2.0277-0.19280.6267-1.19920.8362-0.060.15860.8854-0.23290.647816.31924.0359114.1945
357.1634-3.3859-1.84214.0739-0.19840.9273.10921.62221.4267-1.2725-1.1691-1.14-0.6756-1.20740.39321.03630.0992-0.01860.86680.09411.2135-12.221131.128977.2769
368.2845-6.14131.35587.31071.71945.67271.38190.92912.1962-0.8876-0.5877-3.1111-0.22981.67851.23431.1454-0.71950.37671.25350.28051.3324-3.338922.458767.2428
373.18321.0127-1.4519.0669-6.24714.19150.7753-0.4362-0.99431.09290.6923.029-0.4316-0.9585-0.96771.0925-0.0442-0.04060.6862-0.13311.205-1.299619.623473.8391
384.5542-3.37374.21924.5701-0.44738.087-1.0058-0.19950.063-0.10.81070.1293-0.4418-0.44990.22290.8541-0.09650.24130.70040.0540.813-4.879327.998277.6427
394.9621.4512.9471.9857-2.92553.25830.83560.18211.01891.075-0.97741.766-0.48110.98050.38790.9917-0.11570.04391.377-0.25870.650227.76016.137186.3259
407.62874.55566.74563.82544.18366.01691.07341.786-0.5361.8480.2288-0.70980.9720.8449-0.78520.7615-0.05710.08771.3017-0.24860.902631.778614.728289.5919
418.9441-0.6982-1.93276.08340.1835.9674-0.3612-0.86790.479-0.18560.5915-0.8433-0.58012.5750.19040.5278-0.2490.21340.9718-0.29350.651829.318521.239474.0191
4210.01530.3146-1.18034.4283-2.6466.9303-0.34061.1549-1.593-1.13090.1097-0.79370.32780.0301-0.00590.5668-0.19180.21640.7807-0.33080.702619.362615.386369.7997
434.9516-4.88065.11684.7585-4.36289.32060.15450.0583-1.64561.7874-0.1850.1293-0.51142.13140.02351.0195-0.13050.20371.2537-0.01340.85931.483211.891871.5689
445.3701-0.549-6.10694.2414-1.95877.6568-1.1806-0.4836-1.0006-0.16250.06660.15381.17570.22960.57350.5295-0.19810.22360.6871-0.20360.848818.664215.831880.7803
458.8081-2.98551.11011.7866-3.28228.4461-1.2354-1.1750.684-0.22881.1926-0.4068-0.8588-0.25230.05581.2243-0.01790.19780.8014-0.29030.715511.283831.611995.1631
465.9693-0.97520.23023.7711-4.31694.2597-0.8712-0.30090.35810.3637-1.1406-1.23040.10611.6141.84461.0981-0.25290.10670.8305-0.0460.688922.576728.86680.7622
478.2081-2.3413.87196.53870.88687.070.3041-0.0117-0.0824-0.2307-0.42510.9384-1.22330.2585-0.15590.7083-0.06350.18620.4621-0.24150.6549.151222.425281.1332
487.3366-1.11010.94918.48991.53747.25590.537-0.7103-0.54741.8297-0.7593-0.1859-1.5549-1.1882-0.03291.15310.0580.21370.792-0.06760.44547.716628.04787.2229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 282 through 291 )A282 - 291
2X-RAY DIFFRACTION2chain 'A' and (resid 292 through 313 )A292 - 313
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 339 )A314 - 339
4X-RAY DIFFRACTION4chain 'B' and (resid 1070 through 1092 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1093 through 1129 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1130 through 1155 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1156 through 1176 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1177 through 1194 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1195 through 1259 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1260 through 1280 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 281 through 291 )C281 - 291
12X-RAY DIFFRACTION12chain 'C' and (resid 292 through 313 )C292 - 313
13X-RAY DIFFRACTION13chain 'C' and (resid 314 through 339 )C314 - 339
14X-RAY DIFFRACTION14chain 'D' and (resid 1070 through 1092 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 1093 through 1129 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 1130 through 1142 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 1143 through 1163 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 1164 through 1194 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 1195 through 1218 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 1219 through 1259 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 1260 through 1282 )D0
22X-RAY DIFFRACTION22chain 'E' and (resid 281 through 291 )E281 - 291
23X-RAY DIFFRACTION23chain 'E' and (resid 292 through 313 )E292 - 313
24X-RAY DIFFRACTION24chain 'E' and (resid 314 through 339 )E314 - 339
25X-RAY DIFFRACTION25chain 'F' and (resid 1070 through 1079 )F0
26X-RAY DIFFRACTION26chain 'F' and (resid 1080 through 1092 )F0
27X-RAY DIFFRACTION27chain 'F' and (resid 1093 through 1105 )F0
28X-RAY DIFFRACTION28chain 'F' and (resid 1106 through 1129 )F0
29X-RAY DIFFRACTION29chain 'F' and (resid 1130 through 1163 )F0
30X-RAY DIFFRACTION30chain 'F' and (resid 1164 through 1178 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 1179 through 1194 )F0
32X-RAY DIFFRACTION32chain 'F' and (resid 1195 through 1218 )F0
33X-RAY DIFFRACTION33chain 'F' and (resid 1219 through 1259 )F0
34X-RAY DIFFRACTION34chain 'F' and (resid 1260 through 1280 )F0
35X-RAY DIFFRACTION35chain 'G' and (resid 281 through 286 )G281 - 286
36X-RAY DIFFRACTION36chain 'G' and (resid 287 through 291 )G287 - 291
37X-RAY DIFFRACTION37chain 'G' and (resid 292 through 305 )G292 - 305
38X-RAY DIFFRACTION38chain 'G' and (resid 306 through 339 )G306 - 339
39X-RAY DIFFRACTION39chain 'H' and (resid 1070 through 1079 )H0
40X-RAY DIFFRACTION40chain 'H' and (resid 1080 through 1092 )H0
41X-RAY DIFFRACTION41chain 'H' and (resid 1093 through 1105 )H0
42X-RAY DIFFRACTION42chain 'H' and (resid 1106 through 1129 )H0
43X-RAY DIFFRACTION43chain 'H' and (resid 1130 through 1142 )H0
44X-RAY DIFFRACTION44chain 'H' and (resid 1143 through 1163 )H0
45X-RAY DIFFRACTION45chain 'H' and (resid 1164 through 1194 )H0
46X-RAY DIFFRACTION46chain 'H' and (resid 1195 through 1218 )H0
47X-RAY DIFFRACTION47chain 'H' and (resid 1219 through 1259 )H0
48X-RAY DIFFRACTION48chain 'H' and (resid 1260 through 1280 )H0

+
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