[English] 日本語
Yorodumi
- PDB-5eel: Grb7 SH2 with bicyclic peptide inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eel
TitleGrb7 SH2 with bicyclic peptide inhibitor
Components
  • Bicyclic Peptide Inhibitor
  • Growth factor receptor-bound protein 7
KeywordsSignaling Protein/Peptide / SH2 / inhibitor / bicyclic / Signaling Protein-Peptide complex
Function / homology
Function and homology information


GRB7 events in ERBB2 signaling / RND1 GTPase cycle / RET signaling / stress granule assembly / Tie2 Signaling / phosphatidylinositol binding / Downstream signal transduction / cell projection / epidermal growth factor receptor signaling pathway / Signaling by SCF-KIT ...GRB7 events in ERBB2 signaling / RND1 GTPase cycle / RET signaling / stress granule assembly / Tie2 Signaling / phosphatidylinositol binding / Downstream signal transduction / cell projection / epidermal growth factor receptor signaling pathway / Signaling by SCF-KIT / cytoplasmic stress granule / negative regulation of translation / positive regulation of cell migration / focal adhesion / protein kinase binding / RNA binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Growth factor receptor-bound protein 7 / : / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain ...Growth factor receptor-bound protein 7 / : / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / SH2 domain / SHC Adaptor Protein / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / MALONIC ACID / Growth factor receptor-bound protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.47 Å
AuthorsWatson, G.M. / Gunzburg, M.J. / Wilce, M.C.J. / Wilce, J.A.
CitationJournal: Sci Rep / Year: 2016
Title: Unexpected involvement of staple leads to redesign of selective bicyclic peptide inhibitor of Grb7.
Authors: Gunzburg, M.J. / Kulkarni, K. / Watson, G.M. / Ambaye, N.D. / Del Borgo, M.P. / Brandt, R. / Pero, S.C. / Perlmutter, P. / Wilce, M.C. / Wilce, J.A.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 2.0Dec 26, 2018Group: Data collection / Derived calculations / Polymer sequence
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity_poly / pdbx_struct_oper_list
Item: _chem_comp.mon_nstd_flag / _diffrn_source.pdbx_synchrotron_site ..._chem_comp.mon_nstd_flag / _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Growth factor receptor-bound protein 7
B: Growth factor receptor-bound protein 7
C: Growth factor receptor-bound protein 7
D: Growth factor receptor-bound protein 7
E: Growth factor receptor-bound protein 7
F: Growth factor receptor-bound protein 7
L: Bicyclic Peptide Inhibitor
M: Bicyclic Peptide Inhibitor
N: Bicyclic Peptide Inhibitor
P: Bicyclic Peptide Inhibitor
Q: Bicyclic Peptide Inhibitor
R: Bicyclic Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,88429
Polymers88,94912
Non-polymers93417
Water1,35175
1
A: Growth factor receptor-bound protein 7
M: Bicyclic Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9985
Polymers14,8252
Non-polymers1733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-18 kcal/mol
Surface area6060 Å2
MethodPISA
2
B: Growth factor receptor-bound protein 7
N: Bicyclic Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8944
Polymers14,8252
Non-polymers692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-14 kcal/mol
Surface area6590 Å2
MethodPISA
3
C: Growth factor receptor-bound protein 7
P: Bicyclic Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9985
Polymers14,8252
Non-polymers1733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-21 kcal/mol
Surface area6200 Å2
MethodPISA
4
D: Growth factor receptor-bound protein 7
Q: Bicyclic Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9985
Polymers14,8252
Non-polymers1733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-20 kcal/mol
Surface area6220 Å2
MethodPISA
5
E: Growth factor receptor-bound protein 7
R: Bicyclic Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9985
Polymers14,8252
Non-polymers1733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-19 kcal/mol
Surface area6100 Å2
MethodPISA
6
F: Growth factor receptor-bound protein 7
L: Bicyclic Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9985
Polymers14,8252
Non-polymers1733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-20 kcal/mol
Surface area6350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.228, 95.228, 241.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein / Protein/peptide , 2 types, 12 molecules ABCDEFLMNPQR

#1: Protein
Growth factor receptor-bound protein 7 / B47 / Epidermal growth factor receptor GRB-7 / GRB7 adapter protein


Mass: 13690.711 Da / Num. of mol.: 6 / Fragment: UNP rersidues 415-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14451
#2: Protein/peptide
Bicyclic Peptide Inhibitor


Mass: 1134.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 92 molecules

#3: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 5% v/v Tacsimate pH 5.0, 8% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.47→46.72 Å / Num. obs: 40842 / % possible obs: 99.97 % / Redundancy: 12.9 % / Net I/σ(I): 16.84

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementResolution: 2.47→46.72 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 2048 5.02 %
Rwork0.185 --
obs0.188 40819 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.14 Å2
Refinement stepCycle: LAST / Resolution: 2.47→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5438 0 59 75 5572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075622
X-RAY DIFFRACTIONf_angle_d1.0157515
X-RAY DIFFRACTIONf_dihedral_angle_d15.5322028
X-RAY DIFFRACTIONf_chiral_restr0.037805
X-RAY DIFFRACTIONf_plane_restr0.004981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.52750.30291270.24442531X-RAY DIFFRACTION100
2.5275-2.59070.31081560.23922528X-RAY DIFFRACTION100
2.5907-2.66070.26271280.22752542X-RAY DIFFRACTION100
2.6607-2.7390.26721530.21792517X-RAY DIFFRACTION100
2.739-2.82740.27541370.21582521X-RAY DIFFRACTION100
2.8274-2.92840.23031160.22152585X-RAY DIFFRACTION100
2.9284-3.04570.32281390.22472541X-RAY DIFFRACTION100
3.0457-3.18420.2621210.21552572X-RAY DIFFRACTION100
3.1842-3.35210.20831470.19622549X-RAY DIFFRACTION100
3.3521-3.5620.25921280.19782581X-RAY DIFFRACTION100
3.562-3.83690.22011310.17852593X-RAY DIFFRACTION100
3.8369-4.22280.24131440.15942590X-RAY DIFFRACTION100
4.2228-4.83330.19581350.13472638X-RAY DIFFRACTION100
4.8333-6.08740.18191560.15682642X-RAY DIFFRACTION100
6.0874-46.72380.19391300.17582841X-RAY DIFFRACTION100
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)
17.94375.0098-3.72037.24110.23713.398-0.11990.1440.1082-0.61730.5361-1.3992-0.4831.0585-0.46070.3991-0.01350.04980.5581-0.11140.66419.695251.73499.4442
20.97441.971-0.07654.9433-1.20191.46450.79060.13540.722-0.6548-0.2894-1.4386-1.22450.1441-0.47590.84330.01180.3810.324-0.05350.74440.701361.480997.1988
38.27145.7999-4.08489.3518-6.38654.40920.6536-0.73680.39250.2212-0.4893-0.9809-0.23540.4195-0.1990.55810.0530.09370.3015-0.08370.4622.505748.3923104.5294
44.1312-0.4170.85060.8835-1.39915.16750.4142-0.01620.2112-0.7013-0.3112-0.3796-0.3738-0.0872-0.05530.56390.1220.12030.2527-0.02260.329-2.96848.802197.6304
52.6896-1.79191.34968.89283.4288.32390.62020.1026-0.41140.0022-0.3647-0.20560.63830.1692-0.24320.45420.07210.08070.2643-0.06020.4059-0.145535.55296.8252
66.57383.06574.29291.47152.1093.03640.75560.7623-0.4049-0.5333-0.2653-0.2928-0.02640.2344-0.5780.54790.1930.14420.424-0.09250.42624.191743.697189.0229
76.65132.9552-1.72846.76253.55676.15440.63180.6950.1213-1.362-0.2713-0.7732-1.3212-0.1344-0.4690.86160.18670.22510.3724-0.10060.4949-0.385351.645888.4684
86.5482-3.77914.62592.9548-1.15326.46530.0227-0.18060.21590.2596-0.1550.1807-0.2258-0.77380.1390.2767-0.08310.04850.63910.00510.366762.774471.5668103.6445
94.6946-0.1593-0.89685.45165.5055.7145-0.09970.15620.6685-0.5190.0724-0.2241-0.16520.0851-0.02360.28370.018-0.03440.46180.06130.342361.873761.620698.7576
100.8886-1.31961.10015.7095-2.99778.0690.11040.106-0.3545-0.3773-0.09-0.71090.65460.2584-0.01810.28540.11170.0020.3934-0.00050.393758.743652.275697.1404
114.7337-4.6878-3.95847.00836.22427.14550.70591.50290.2636-1.37610.608-0.0382-1.28161.2438-0.93130.52670.02630.0250.47690.05950.353153.509667.072989.3827
123.33852.4683-0.08643.03450.47965.9857-0.0544-0.2555-0.21170.08760.0935-0.4447-0.00170.1295-0.03840.2140.0531-0.03870.227-0.01960.181249.600258.956797.6309
134.85731.8551-0.40275.3264-1.87233.10070.10570.28950.79590.22850.1870.74-1.0073-0.5249-0.14140.3210.0558-0.05030.3337-0.02420.3445.309370.7247102.5401
148.17027.7203-7.27967.2988-6.97919.06580.32280.0417-0.23410.5627-0.08850.0933-0.09510.245-0.27850.22130.1284-0.03920.3241-0.03540.308751.34362.7134109.2111
154.6831-3.0474-2.40738.99510.73685.7866-0.6370.1834-0.14230.20630.194-0.07260.7280.89880.38070.29170.0919-0.04030.370.01250.245652.175654.6867105.768
166.9794-6.9364-0.61929.41861.96962.758-0.0254-0.58870.638-0.3070.1037-1.0663-0.93740.1872-0.07530.4556-0.07440.1560.3821-0.09440.467314.204926.931576.0463
171.2881-0.42350.01462.5473-0.0920.0861-0.14620.284-0.26170.0111-0.69460.76980.0723-1.3161-0.46090.3660.21420.41280.4657-0.81140.2818.216415.29372.6669
184.322-1.1249-1.48837.0523-2.65498.9374-0.01970.4085-0.1431-0.4747-0.51930.04150.3532-0.63420.37530.47150.06890.04830.5709-0.27950.45186.613423.729374.4722
193.4360.7374-1.09011.95472.25446.5016-0.2220.2186-0.4692-0.2065-0.48780.0248-0.4644-1.10480.5950.44840.12090.01020.6899-0.30180.54981.100425.78675.6341
205.1422-0.8197-1.35348.02795.84087.66160.03450.33170.0348-0.8802-0.21570.1006-1.3133-0.9494-0.14610.90740.5082-0.04520.7175-0.23210.47291.266640.271876.5385
212.4413-2.0419-1.07874.47320.73034.6952-0.25940.2078-0.27780.4245-0.15310.28330.1454-0.3970.36610.37150.02430.05270.5738-0.26920.50595.68627.435584.1209
224.6120.771-3.92684.623-2.32797.77-0.2650.0338-0.6660.0155-0.0281-0.81920.44250.02440.24370.3204-0.0737-0.02420.2598-0.01760.604952.358611.294757.3586
233.20954.2052-1.53017.9727-4.99828.21740.1153-1.1093-0.19531.2693-0.263-1.2281-0.05490.21050.20190.5195-0.2183-0.07850.5892-0.00920.405649.055815.535668.5437
246.85071.6328-1.56329.32510.17329.5321-0.23840.8132-0.9532-1.0436-0.1266-0.31550.3063-0.22260.39090.3727-0.1412-0.05340.4013-0.04450.48853.590917.455449.6461
253.5576-3.947-3.18878.48446.75387.9336-0.1006-0.40780.13680.4478-0.32860.19690.6109-0.27960.36380.2248-0.1372-0.02910.33830.00730.471248.850820.331761.1648
261.9652-1.34641.1325.19280.41250.9653-0.0042-0.25740.0023-0.5117-0.3159-0.1623-0.70230.69150.08740.4912-0.2512-0.14290.38510.04850.37852.330724.788252.3601
279.79411.24065.71349.6006-5.54327.4950.65731.00940.9296-1.87370.0662-0.5101-0.02351.2601-0.68990.6334-0.20560.22330.5285-0.06240.603463.664129.260546.4506
288.3601-3.79710.37623.15052.58526.1830.29290.1601-0.0157-0.4856-0.10290.3961-0.1320.0803-0.13810.4653-0.1532-0.0590.32020.10970.467759.202731.294552.2864
292.5521-0.60430.89126.44445.7255.83630.02180.1713-0.06780.3318-0.0285-0.65720.1086-0.0886-0.08520.3096-0.1388-0.01480.30040.05080.473261.858625.446361.0127
306.89771.36742.16487.9718-0.47414.62020.4707-0.808-0.14990.6681-0.30170.41830.06210.0201-0.22660.3996-0.2255-0.06930.40510.07950.544654.261622.958265.0754
311.22512.20510.72034.02891.63165.15950.2602-0.1528-0.3718-0.0521-0.0759-0.330.73470.6905-0.08480.46740.1746-0.13220.2577-0.02770.365439.821560.255377.82
326.31690.86385.19743.16720.45274.8049-0.2069-0.72980.61660.38110.2985-0.1646-0.9715-0.5320.01970.54880.2169-0.13450.4039-0.09730.262639.700769.47685.9079
336.99545.3042.01387.54123.05696.6863-0.1421-0.08210.15020.8348-0.1004-0.5561-0.90160.17350.26530.36540.0749-0.16090.2969-0.05120.320139.206869.987477.7432
344.74640.58844.23762.43411.89554.5835-0.4976-0.4717-1.11420.38310.57230.25490.155-1.2362-0.27270.5233-0.11730.11230.45940.05290.542125.908458.140982.3648
351.7101-0.89370.01980.47240.1793.5575-0.1275-0.13040.61410.4544-0.68310.1538-0.5038-0.3510.55010.56620.0539-0.25470.2987-0.07460.393234.067972.191477.3543
368.8615-0.09080.61428.0522-0.76738.65530.16440.2653-0.6797-0.0231-0.04420.49570.6623-1.0264-0.0510.2317-0.0126-0.0490.3515-0.03550.262324.683462.061370.3632
374.7468-1.04590.88856.2774-5.59337.9762-0.17390.35530.3009-0.27760.12570.3225-0.21590.23630.07430.27130.0626-0.14020.3501-0.07190.261432.921867.596665.6543
387.5512-4.96224.22484.1323-5.02528.3417-0.59920.02750.1490.2812-0.1108-0.1435-0.33880.67820.58570.37030.0332-0.1520.4926-0.09450.376340.93269.140273.2212
398.3589-3.2374-1.88131.59150.36168.64350.1406-0.1962-0.03680.1987-0.0543-0.21280.05940.0856-0.1030.345-0.0696-0.08030.16370.02410.259332.99073.56668.4461
404.04312.218-4.58616.9324-1.47556.20790.1629-0.3952-0.47260.4654-0.647-0.0084-0.22720.03360.36320.2417-0.0394-0.04170.2542-0.03990.265726.77976.255567.8203
417.95012.8299-4.15941.3356-2.86587.40920.0994-0.140.64230.0037-0.2132-0.0107-0.2785-0.21970.09850.2712-0.0598-0.01310.1759-0.0290.426327.773211.637163.577
422.27484.2904-3.14638.6636-5.344.97120.0154-0.5725-0.0055-1.0056-0.01041.9170.7267-1.39260.0830.3935-0.1954-0.02030.4516-0.03050.62427.43381.293264.5114
436.72421.3363-0.67723.19610.71456.69060.10760.1436-0.15080.0714-0.17890.51660.2181-0.4260.09250.2424-0.0486-0.00410.163-0.03740.286618.01452.900257.3494
448.6005-5.41195.45685.9345-1.14177.0779-0.11590.30360.01450.16650.0179-0.2488-0.11140.4310.12390.205-0.0528-0.00710.20560.01320.279829.6396.275157.125
458.10677.23721.06429.12164.67466.92680.5225-0.00770.13410.4433-0.3972-0.5054-0.3254-0.3854-0.3550.3110.03550.10070.2096-0.03820.437918.624215.472866.8857
467.0638-1.21150.82655.4266-6.06447.92330.73520.3548-0.064-1.0134-0.1558-0.0064-0.09520.0174-0.56630.43980.11150.04740.2741-0.06720.4394-9.643746.7477101.9461
474.16562.0851-3.60297.7335-0.50133.3684-0.03260.2939-0.392-0.1117-0.078-0.0644-0.2579-0.70670.09530.25420.0131-0.05690.3475-0.01290.284643.74259.696191.6565
488.0868-4.80930.48848.376-2.47423.07530.44090.2318-0.6049-0.4001-0.30921.2472-0.5682-0.8343-0.08120.59210.3708-0.09331.2841-0.50190.9981-5.181327.615269.7135
497.28252.9094-6.73687.6446-1.25156.5534-0.0880.67070.389-1.30270.49820.6549-0.1178-0.3607-0.42490.4443-0.3479-0.19050.41430.20260.830845.670426.8850.7391
507.03427.36481.50039.4509-2.18288.5494-0.2999-1.5951.22640.62640.20470.75210.294-0.663-0.0030.37290.1952-0.05840.6768-0.08360.317622.208669.436179.1242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 426 THROUGH 437 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 438 THROUGH 454 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 455 THROUGH 466 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 467 THROUGH 487 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 488 THROUGH 504 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 505 THROUGH 514 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 515 THROUGH 529 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 421 THROUGH 428 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 429 THROUGH 437 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 438 THROUGH 459 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 460 THROUGH 466 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 467 THROUGH 487 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 488 THROUGH 504 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 505 THROUGH 514 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 515 THROUGH 529 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 427 THROUGH 437 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 438 THROUGH 447 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 448 THROUGH 466 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 467 THROUGH 487 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 488 THROUGH 504 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 505 THROUGH 532 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 428 THROUGH 447 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 448 THROUGH 454 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 455 THROUGH 466 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 467 THROUGH 475 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 476 THROUGH 487 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 488 THROUGH 494 )
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 495 THROUGH 504 )
29X-RAY DIFFRACTION29CHAIN 'D' AND (RESID 505 THROUGH 514 )
30X-RAY DIFFRACTION30CHAIN 'D' AND (RESID 515 THROUGH 529 )
31X-RAY DIFFRACTION31CHAIN 'E' AND (RESID 429 THROUGH 437 )
32X-RAY DIFFRACTION32CHAIN 'E' AND (RESID 438 THROUGH 447 )
33X-RAY DIFFRACTION33CHAIN 'E' AND (RESID 448 THROUGH 459 )
34X-RAY DIFFRACTION34CHAIN 'E' AND (RESID 460 THROUGH 466 )
35X-RAY DIFFRACTION35CHAIN 'E' AND (RESID 467 THROUGH 475 )
36X-RAY DIFFRACTION36CHAIN 'E' AND (RESID 476 THROUGH 504 )
37X-RAY DIFFRACTION37CHAIN 'E' AND (RESID 505 THROUGH 519 )
38X-RAY DIFFRACTION38CHAIN 'E' AND (RESID 520 THROUGH 530 )
39X-RAY DIFFRACTION39CHAIN 'F' AND (RESID 427 THROUGH 448 )
40X-RAY DIFFRACTION40CHAIN 'F' AND (RESID 449 THROUGH 466 )
41X-RAY DIFFRACTION41CHAIN 'F' AND (RESID 467 THROUGH 482 )
42X-RAY DIFFRACTION42CHAIN 'F' AND (RESID 483 THROUGH 492 )
43X-RAY DIFFRACTION43CHAIN 'F' AND (RESID 493 THROUGH 514 )
44X-RAY DIFFRACTION44CHAIN 'F' AND (RESID 515 THROUGH 530 )
45X-RAY DIFFRACTION45CHAIN 'L' AND (RESID 1 THROUGH 8 )
46X-RAY DIFFRACTION46CHAIN 'M' AND (RESID 1 THROUGH 8 )
47X-RAY DIFFRACTION47CHAIN 'N' AND (RESID 1 THROUGH 8 )
48X-RAY DIFFRACTION48CHAIN 'P' AND (RESID 1 THROUGH 8 )
49X-RAY DIFFRACTION49CHAIN 'Q' AND (RESID 1 THROUGH 8 )
50X-RAY DIFFRACTION50CHAIN 'R' AND (RESID 1 THROUGH 8 )

+
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