[English] 日本語
Yorodumi
- PDB-7xge: Crystal structure of MCL-1 in complex with computationally design... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xge
TitleCrystal structure of MCL-1 in complex with computationally designed inhibitor protein
Components
  • BCL-xL and MCL-1 dual binder 2
  • Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsAPOTOSIS / DE NOVO PROTEIN / computational design
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein transmembrane transporter activity ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein transmembrane transporter activity / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Apoptosis regulator, Mcl-1 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 ...Apoptosis regulator, Mcl-1 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsOh, B.-H. / Kim, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: Computational design of an apoptogenic protein that binds BCL-xL and MCL-1 simultaneously and potently.
Authors: Kim, S. / Park, H.S. / Oh, B.H.
History
DepositionApr 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BCL-xL and MCL-1 dual binder 2
B: Induced myeloid leukemia cell differentiation protein Mcl-1
C: BCL-xL and MCL-1 dual binder 2
D: Induced myeloid leukemia cell differentiation protein Mcl-1
E: BCL-xL and MCL-1 dual binder 2
F: Induced myeloid leukemia cell differentiation protein Mcl-1
G: BCL-xL and MCL-1 dual binder 2
H: Induced myeloid leukemia cell differentiation protein Mcl-1


Theoretical massNumber of molelcules
Total (without water)148,0678
Polymers148,0678
Non-polymers00
Water3,369187
1
A: BCL-xL and MCL-1 dual binder 2
B: Induced myeloid leukemia cell differentiation protein Mcl-1


Theoretical massNumber of molelcules
Total (without water)37,0172
Polymers37,0172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-14 kcal/mol
Surface area15600 Å2
MethodPISA
2
C: BCL-xL and MCL-1 dual binder 2
D: Induced myeloid leukemia cell differentiation protein Mcl-1


Theoretical massNumber of molelcules
Total (without water)37,0172
Polymers37,0172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-10 kcal/mol
Surface area14690 Å2
MethodPISA
3
E: BCL-xL and MCL-1 dual binder 2
F: Induced myeloid leukemia cell differentiation protein Mcl-1


Theoretical massNumber of molelcules
Total (without water)37,0172
Polymers37,0172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-13 kcal/mol
Surface area14230 Å2
MethodPISA
4
G: BCL-xL and MCL-1 dual binder 2
H: Induced myeloid leukemia cell differentiation protein Mcl-1


Theoretical massNumber of molelcules
Total (without water)37,0172
Polymers37,0172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-11 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.990, 74.770, 92.160
Angle α, β, γ (deg.)70.830, 89.590, 67.580
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 5 or resid 8...
21(chain C and (resid 4 through 5 or resid 8...
31(chain E and (resid 4 through 5 or resid 8...
41(chain G and (resid 4 through 5 or resid 8...
12(chain B and (resid 4 through 25 or resid 36...
22(chain D and (resid 4 through 25 or resid 36...
32(chain F and (resid 4 through 25 or resid 36...
42(chain H and (resid 4 through 38 or resid 40...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 5 or resid 8...A4 - 5
121(chain A and (resid 4 through 5 or resid 8...A8 - 9
131(chain A and (resid 4 through 5 or resid 8...A0
141(chain A and (resid 4 through 5 or resid 8...A40
151(chain A and (resid 4 through 5 or resid 8...A47 - 71
161(chain A and (resid 4 through 5 or resid 8...A73
171(chain A and (resid 4 through 5 or resid 8...A73
181(chain A and (resid 4 through 5 or resid 8...A75 - 98
191(chain A and (resid 4 through 5 or resid 8...A104 - 10113
1101(chain A and (resid 4 through 5 or resid 8...A117
1111(chain A and (resid 4 through 5 or resid 8...A4 - 171
1121(chain A and (resid 4 through 5 or resid 8...A129 - 130
1131(chain A and (resid 4 through 5 or resid 8...A4 - 171
1141(chain A and (resid 4 through 5 or resid 8...A136 - 1
1151(chain A and (resid 4 through 5 or resid 8...A157 - 15
1161(chain A and (resid 4 through 5 or resid 8...A161 - 164
211(chain C and (resid 4 through 5 or resid 8...C4 - 5
221(chain C and (resid 4 through 5 or resid 8...C8 - 9
231(chain C and (resid 4 through 5 or resid 8...C11 - 17
241(chain C and (resid 4 through 5 or resid 8...C19 - 35
251(chain C and (resid 4 through 5 or resid 8...C43 - 44
261(chain C and (resid 4 through 5 or resid 8...C7 - 71
271(chain C and (resid 4 through 5 or resid 8...C4 - 164
281(chain C and (resid 4 through 5 or resid 8...C75 - 98
291(chain C and (resid 4 through 5 or resid 8...C0
2101(chain C and (resid 4 through 5 or resid 8...C4 - 164
2111(chain C and (resid 4 through 5 or resid 8...C115
2121(chain C and (resid 4 through 5 or resid 8...C115
2131(chain C and (resid 4 through 5 or resid 8...C117
2141(chain C and (resid 4 through 5 or resid 8...C132 - 133
2151(chain C and (resid 4 through 5 or resid 8...C142 - 155
2161(chain C and (resid 4 through 5 or resid 8...C157 - 15
2171(chain C and (resid 4 through 5 or resid 8...C161 - 164
311(chain E and (resid 4 through 5 or resid 8...E4 - 5
321(chain E and (resid 4 through 5 or resid 8...E8 - 9
331(chain E and (resid 4 through 5 or resid 8...E11 - 17
341(chain E and (resid 4 through 5 or resid 8...E19 - 35
351(chain E and (resid 4 through 5 or resid 8...E43 - 44
361(chain E and (resid 4 through 5 or resid 8...E7 - 71
371(chain E and (resid 4 through 5 or resid 8...E4 - 164
381(chain E and (resid 4 through 5 or resid 8...E75 - 98
391(chain E and (resid 4 through 5 or resid 8...E0
3101(chain E and (resid 4 through 5 or resid 8...E4 - 164
3111(chain E and (resid 4 through 5 or resid 8...E115
3121(chain E and (resid 4 through 5 or resid 8...E115
3131(chain E and (resid 4 through 5 or resid 8...E117
3141(chain E and (resid 4 through 5 or resid 8...E132 - 133
3151(chain E and (resid 4 through 5 or resid 8...E142 - 155
3161(chain E and (resid 4 through 5 or resid 8...E157 - 15
3171(chain E and (resid 4 through 5 or resid 8...E161 - 164
411(chain G and (resid 4 through 5 or resid 8...G4 - 5
421(chain G and (resid 4 through 5 or resid 8...G8 - 9
431(chain G and (resid 4 through 5 or resid 8...G11 - 17
441(chain G and (resid 4 through 5 or resid 8...G43 - 44
451(chain G and (resid 4 through 5 or resid 8...G47 - 71
461(chain G and (resid 4 through 5 or resid 8...G7 - 71
471(chain G and (resid 4 through 5 or resid 8...G73
481(chain G and (resid 4 through 5 or resid 8...G700 - 102
491(chain G and (resid 4 through 5 or resid 8...G4 - 1091
4101(chain G and (resid 4 through 5 or resid 8...G4 - 167
4111(chain G and (resid 4 through 5 or resid 8...G115
4121(chain G and (resid 4 through 5 or resid 8...G4 - 167
4131(chain G and (resid 4 through 5 or resid 8...G129 - 130
4141(chain G and (resid 4 through 5 or resid 8...G133
4151(chain G and (resid 4 through 5 or resid 8...G4 - 167
4161(chain G and (resid 4 through 5 or resid 8...G142 - 155
4171(chain G and (resid 4 through 5 or resid 8...G157 - 159
4181(chain G and (resid 4 through 5 or resid 8...G161 - 164
112(chain B and (resid 4 through 25 or resid 36...B4 - 25
122(chain B and (resid 4 through 25 or resid 36...B36 - 38
132(chain B and (resid 4 through 25 or resid 36...B40 - 42
142(chain B and (resid 4 through 25 or resid 36...B44 - 75
152(chain B and (resid 4 through 25 or resid 36...B4 - 153
162(chain B and (resid 4 through 25 or resid 36...B112 - 115
172(chain B and (resid 4 through 25 or resid 36...B117 - 152
212(chain D and (resid 4 through 25 or resid 36...D4 - 25
222(chain D and (resid 4 through 25 or resid 36...D36 - 38
232(chain D and (resid 4 through 25 or resid 36...D4 - 154
242(chain D and (resid 4 through 25 or resid 36...D4 - 154
252(chain D and (resid 4 through 25 or resid 36...D112 - 1
262(chain D and (resid 4 through 25 or resid 36...D11715
272(chain D and (resid 4 through 25 or resid 36...D117 - 152
312(chain F and (resid 4 through 25 or resid 36...F4 - 25
322(chain F and (resid 4 through 25 or resid 36...F36 - 38
332(chain F and (resid 4 through 25 or resid 36...F40 - 42
342(chain F and (resid 4 through 25 or resid 36...F112 - 115
352(chain F and (resid 4 through 25 or resid 36...F4 - 154
362(chain F and (resid 4 through 25 or resid 36...F112 - 115
372(chain F and (resid 4 through 25 or resid 36...F117 - 152
412(chain H and (resid 4 through 38 or resid 40...H4 - 38
422(chain H and (resid 4 through 38 or resid 40...H40 - 42
432(chain H and (resid 4 through 38 or resid 40...H44 - 75
442(chain H and (resid 4 through 38 or resid 40...H77 - 110
452(chain H and (resid 4 through 38 or resid 40...H112 - 115
462(chain H and (resid 4 through 38 or resid 40...H117 - 152

NCS ensembles :
ID
1
2

-
Components

#1: Protein
BCL-xL and MCL-1 dual binder 2


Mass: 19149.291 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Protein
Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 17867.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07820
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 6,000 (w/v), 0.1M Magnesium chloride, 0.1M ADA (pH 6.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97959 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.38→29.46 Å / Num. obs: 61301 / % possible obs: 97.36 % / Redundancy: 3.6 % / CC1/2: 0.99 / Net I/σ(I): 14
Reflection shellResolution: 2.38→2.47 Å / Num. unique obs: 6115 / CC1/2: 0.721

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: design model

Resolution: 2.38→29.46 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 3064 5 %
Rwork0.2024 58223 -
obs0.2042 61287 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.94 Å2 / Biso mean: 70.892 Å2 / Biso min: 32.82 Å2
Refinement stepCycle: final / Resolution: 2.38→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9769 0 0 187 9956
Biso mean---57.69 -
Num. residues----1219
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1300X-RAY DIFFRACTION4.979TORSIONAL
12C1300X-RAY DIFFRACTION4.979TORSIONAL
13E1300X-RAY DIFFRACTION4.979TORSIONAL
14G1300X-RAY DIFFRACTION4.979TORSIONAL
21B1572X-RAY DIFFRACTION4.979TORSIONAL
22D1572X-RAY DIFFRACTION4.979TORSIONAL
23F1572X-RAY DIFFRACTION4.979TORSIONAL
24H1572X-RAY DIFFRACTION4.979TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.38-2.420.3181400.2922673281397
2.42-2.460.30281370.27152596273397
2.46-2.50.28271400.26282666280697
2.5-2.540.28521380.25332612275097
2.54-2.590.2941380.25162619275797
2.59-2.650.27751390.24582647278697
2.65-2.70.27861380.24192629276797
2.7-2.770.3121400.24832663280397
2.77-2.840.30541400.2452662280297
2.84-2.910.3011380.26082632277098
2.91-30.3131390.23712641278098
3-3.090.27061420.23772684282698
3.09-3.210.28991380.23622633277198
3.21-3.330.27451380.23572627276597
3.33-3.480.24931400.22872661280197
3.49-3.670.27621390.20472632277197
3.67-3.90.23041390.1922643278298
3.9-4.20.18011410.17552680282197
4.2-4.620.20661380.16212627276597
4.62-5.280.23431390.17582641278097
5.28-6.640.21551410.20882663280498
6.65-29.460.18861420.15452692283499
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)
14.03932.0204-0.29352.0655-0.27741.8250.11550.35330.31970.03740.10250.040.07480.0489-0.21230.39750.0342-0.0120.35870.03390.4092-20.792335.327532.6189
24.42-0.0266-0.66842.06640.54632.8652-0.20180.1114-0.73040.30990.0964-0.19460.56490.1335-0.07250.47680.0207-0.04570.34060.0330.4724-25.424325.756737.0727
34.6761-0.40772.99920.30690.18712.59921.12773.07650.586-1.2267-0.9705-1.0934-0.173.0780.56650.98610.32040.10991.5325-0.05611.1294-0.330227.298215.2801
41.3804-0.1239-0.00041.54560.51942.51760.12650.8406-0.25060.10990.0808-0.08480.1206-0.2728-0.14570.52510.01-0.06980.4624-0.02610.5256-29.957223.410228.4191
52.0334-1.3311-0.24884.38590.73761.92070.0528-0.8487-0.3011.8589-0.1713-0.91560.40250.5050.01090.80070.0261-0.17310.73110.10050.5496-9.892739.619156.4338
61.3020.4048-0.13230.7216-0.24810.25170.9664-0.5017-0.1379-0.5284-0.5910.8805-0.21430.59940.00561.40090.2057-0.15110.94930.10940.9543-10.29637.095665.4024
72.3508-0.5987-0.10291.7880.22861.89320.0519-0.26-0.47460.44830.0753-0.3050.17690.4902-0.22220.53450.0144-0.07690.52440.04730.58-11.210134.741443.8948
80.365-0.5554-0.61192.00610.62941.35720.0025-0.14580.06020.24250.1384-0.58490.21480.4603-0.14510.44240.05-0.14110.54320.0440.497-9.089239.372247.5278
92.4151-0.79261.84276.61442.0485.02560.4747-0.3702-0.28541.3209-0.76081.1840.5692-0.37150.01750.6786-0.00740.10060.58810.0680.5198-25.427240.177653.3859
104.6264-0.24231.01072.4870.65253.93580.12550.21460.0931-0.2726-0.10480.00010.0041-0.2216-0.04210.3635-0.01350.04950.39280.02450.4156-26.040467.694541.1115
113.2574-3.1624-3.27884.22924.32664.420.134-0.991-1.0859-0.4499-0.0637-0.91491.24731.36960.5190.8439-0.1014-0.42311.8769-0.1941.8318-8.871178.654763.8623
122.038-1.1906-2.05382.95510.83922.00850.0577-0.1551-0.348-0.0669-0.01070.0991-0.0975-0.52640.21380.40370.01870.05920.5736-0.02260.5649-33.196773.501349.4439
132.13761.36120.18725.34980.18222.992-0.10630.95630.3156-1.06720.1811-0.3352-0.08380.6629-0.09680.6219-0.05890.1690.81170.05840.5208-8.07662.61822.439
147.8356-2.2091-4.5797.5395-1.58133.89870.54460.46880.7842-1.41010.0747-1.2849-1.05180.8055-0.32260.881-0.4078-0.1311.44520.35091.1061-7.358571.142516.4177
151.82850.12140.14121.53211.09443.3791-0.04360.64130.6029-0.9834-0.07910.1654-0.9704-0.1612-0.07260.7917-0.09340.03380.72950.20910.5673-18.024368.976422.6702
166.7283-0.77540.94771.5980.04032.3775-0.121-0.43451.0906-0.06640.1278-0.3321-0.47680.5984-0.06160.5153-0.12020.09460.5753-0.05870.7116-9.727273.55941.2166
172.63391.0480.09721.93240.07933.06150.1604-0.14040.0704-0.2647-0.0027-0.5390.31050.4317-0.14610.47830.05740.06720.4935-0.01010.5952-10.85359.325939.676
182.18170.40480.62261.96571.02632.03440.01460.1793-0.0981-0.30340.1916-0.6083-0.04760.4132-0.10730.4636-0.060.09650.52620.03030.4789-9.332562.803131.2556
193.8571-1.4946-1.95336.22720.91273.1370.53391.0416-0.124-0.839-0.93270.8837-0.6976-0.44480.10420.73020.035-0.08680.6687-0.04340.4299-24.001259.697621.7191
203.9979-0.2407-1.9212.10541.13043.86290.36980.09650.4421-0.4490.0081-0.2984-0.2672-0.0215-0.40560.4739-0.03550.00830.5085-0.00790.4195-35.370229.51549.551
214.6255-0.7751-1.11643.3420.83583.80960.10530.51970.06280.0451-0.16740.00270.4132-0.3694-0.05740.4277-0.035-0.05880.42930.06410.4115-43.738426.35165.4123
223.9524-0.6645-0.75732.38760.35574.5673-0.1137-0.0557-0.5980.23020.2838-0.15841.12380.5114-0.07790.59950.0294-0.15590.4105-0.00910.6185-33.486916.86528.3459
231.42570.66851.60711.8066-0.05452.50490.1771-0.14040.2988-0.01070.142-0.36810.08350.0282-0.24110.4073-0.0344-0.02040.5662-0.03180.4884-33.448127.081119.5123
242.2448-2.32132.80232.427-3.05384.34210.75160.0742-0.5532-0.4161-0.31860.44850.0927-0.5047-0.44931.16930.2608-0.17841.6676-0.03951.1468-13.626412.28985.4475
251.9329-0.0267-0.42561.61930.67682.49010.06330.3049-1.0591-0.3205-0.09180.40721.2113-0.49430.04270.7309-0.0849-0.06250.5515-0.16590.8389-51.717512.839-7.3386
263.5818-0.7034-0.71972.10610.32473.80030.0359-0.0697-0.22650.0285-0.06010.39490.4004-0.5491-0.05230.5341-0.1165-0.07130.61520.0070.5384-54.253824.67546.2052
272.01780.1412-0.26432.0087-0.09875.35240.15630.2554-0.2943-0.0826-0.03910.22080.5815-0.34120.0140.4975-0.064-0.03030.3797-0.08820.4953-51.679420.0732-4.7975
284.14461.1901-0.17972.60720.42122.12060.14250.15430.16040.0164-0.01620.1281-0.1258-0.0684-0.07960.3880.05280.02080.40530.03420.3974-43.838346.4021-21.2327
291.8716-0.6268-1.13631.7323-0.90123.73120.04440.576-0.1975-0.1520.1459-0.265-0.2782-0.0272-0.13330.43030.1020.05760.50660.05690.3932-37.93147.5572-31.7755
301.9845-0.65411.29792.1553-0.94732.87580.1426-0.46221.1710.8976-0.23750.1522-1.0676-0.2217-0.15530.91450.17440.24780.6758-0.16940.8378-55.648754.90541.2451
312.2855-0.8190.88041.29510.12165.513-0.2258-0.11111.15040.45860.21710.4185-2.14520.39490.37740.93130.02830.13390.4678-0.07451.064-47.992760.1433-5.6643
323.11050.90560.45683.13360.23482.63940.27930.31420.31110.2127-0.20340.7105-0.2218-0.6147-0.06650.4930.11020.11790.584-0.00830.5445-57.841445.4625-14.3146
331.9936-0.28730.70762.0573-0.01482.50270.13020.2540.0950.1219-0.1410.7044-0.427-0.7290.07340.5830.17830.05280.6169-0.02250.7157-57.598253.3165-10.9849
341.76020.61421.20422.007-0.35571.49430.2554-0.5803-0.25330.31450.0480.5267-0.2566-0.7624-0.17120.57140.14790.12950.6098-0.07560.4809-55.215145.5159-0.8207
351.2072-0.9173-0.85185.2923-3.25118.71440.5591-0.01070.20620.5816-0.5602-0.1507-1.37172.45810.03580.6516-0.0796-0.03030.6032-0.07470.5096-40.396552.2679-0.3131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 77 )A4 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 120 )A78 - 120
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 125 )A121 - 125
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 171 )A126 - 171
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 23 )B4 - 23
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 35 )B24 - 35
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 92 )B36 - 92
8X-RAY DIFFRACTION8chain 'B' and (resid 93 through 140 )B93 - 140
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 153 )B141 - 153
10X-RAY DIFFRACTION10chain 'C' and (resid 4 through 120 )C4 - 120
11X-RAY DIFFRACTION11chain 'C' and (resid 121 through 125 )C121 - 125
12X-RAY DIFFRACTION12chain 'C' and (resid 126 through 164 )C126 - 164
13X-RAY DIFFRACTION13chain 'D' and (resid 4 through 23 )D4 - 23
14X-RAY DIFFRACTION14chain 'D' and (resid 24 through 35 )D24 - 35
15X-RAY DIFFRACTION15chain 'D' and (resid 36 through 55 )D36 - 55
16X-RAY DIFFRACTION16chain 'D' and (resid 56 through 71 )D56 - 71
17X-RAY DIFFRACTION17chain 'D' and (resid 72 through 92 )D72 - 92
18X-RAY DIFFRACTION18chain 'D' and (resid 93 through 140 )D93 - 140
19X-RAY DIFFRACTION19chain 'D' and (resid 141 through 154 )D141 - 154
20X-RAY DIFFRACTION20chain 'E' and (resid 4 through 35 )E4 - 35
21X-RAY DIFFRACTION21chain 'E' and (resid 36 through 78 )E36 - 78
22X-RAY DIFFRACTION22chain 'E' and (resid 79 through 117 )E79 - 117
23X-RAY DIFFRACTION23chain 'E' and (resid 118 through 159 )E118 - 159
24X-RAY DIFFRACTION24chain 'E' and (resid 160 through 164 )E160 - 164
25X-RAY DIFFRACTION25chain 'F' and (resid 4 through 55 )F4 - 55
26X-RAY DIFFRACTION26chain 'F' and (resid 56 through 92 )F56 - 92
27X-RAY DIFFRACTION27chain 'F' and (resid 93 through 154 )F93 - 154
28X-RAY DIFFRACTION28chain 'G' and (resid 4 through 125 )G4 - 125
29X-RAY DIFFRACTION29chain 'G' and (resid 126 through 167 )G126 - 167
30X-RAY DIFFRACTION30chain 'H' and (resid 4 through 23 )H4 - 23
31X-RAY DIFFRACTION31chain 'H' and (resid 24 through 55 )H24 - 55
32X-RAY DIFFRACTION32chain 'H' and (resid 56 through 92 )H56 - 92
33X-RAY DIFFRACTION33chain 'H' and (resid 93 through 115 )H93 - 115
34X-RAY DIFFRACTION34chain 'H' and (resid 116 through 140 )H116 - 140
35X-RAY DIFFRACTION35chain 'H' and (resid 141 through 152 )H141 - 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://pdbjlvh1.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