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- PDB-4w9d: pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4... -

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Basic information

Entry
Database: PDB / ID: 4w9d
TitlepVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methyloxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 3)
Components
  • Transcription elongation factor B polypeptide 1
  • Transcription elongation factor B polypeptide 2
  • Von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / protein complex / ubiquitin ligase / hypoxia inducible factor / transcription
Function / homology
Function and homology information


regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / transcription elongation factor activity / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / transcription elongation factor activity / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / cell morphogenesis / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / Replication of the SARS-CoV-2 genome / protein-macromolecule adaptor activity / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / amyloid fibril formation / molecular adaptor activity / protein stabilization / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain ...von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SKP1/BTB/POZ domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3JK / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGadd, M.S. / Hewitt, S. / Galdeano, C. / van Molle, I. / Ciulli, A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
European Research CouncilERC-2012-StG-311460
Biotechnology and Biological Sciences Research CouncilBBSRC BB/G023123/1 United Kingdom
Marie Sklodowska-Curie ActionsEC PIEF-GA-2012-328030
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor ...Title: Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities.
Authors: Galdeano, C. / Gadd, M.S. / Soares, P. / Scaffidi, S. / Van Molle, I. / Birced, I. / Hewitt, S. / Dias, D.M. / Ciulli, A.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription elongation factor B polypeptide 2
B: Transcription elongation factor B polypeptide 1
C: Von Hippel-Lindau disease tumor suppressor
D: Transcription elongation factor B polypeptide 2
E: Transcription elongation factor B polypeptide 1
F: Von Hippel-Lindau disease tumor suppressor
G: Transcription elongation factor B polypeptide 2
H: Transcription elongation factor B polypeptide 1
I: Von Hippel-Lindau disease tumor suppressor
J: Transcription elongation factor B polypeptide 2
K: Transcription elongation factor B polypeptide 1
L: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,54716
Polymers166,94912
Non-polymers1,5984
Water5,062281
1
A: Transcription elongation factor B polypeptide 2
B: Transcription elongation factor B polypeptide 1
C: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1374
Polymers41,7373
Non-polymers3991
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-39 kcal/mol
Surface area16230 Å2
MethodPISA
2
D: Transcription elongation factor B polypeptide 2
E: Transcription elongation factor B polypeptide 1
F: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1374
Polymers41,7373
Non-polymers3991
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-38 kcal/mol
Surface area16370 Å2
MethodPISA
3
G: Transcription elongation factor B polypeptide 2
H: Transcription elongation factor B polypeptide 1
I: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1374
Polymers41,7373
Non-polymers3991
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-39 kcal/mol
Surface area16650 Å2
MethodPISA
4
J: Transcription elongation factor B polypeptide 2
K: Transcription elongation factor B polypeptide 1
L: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1374
Polymers41,7373
Non-polymers3991
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-38 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.901, 93.901, 365.869
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

21I-411-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41J
12B
22E
32H
42K
13C
23F
33I
43L
14C
24F
34I
15C
25F
35I
45L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 999
2114D1 - 999
3114G1 - 999
4114J1 - 999
1124B1 - 999
2124E1 - 999
3124H1 - 999
4124K1 - 999
1134C1 - 169
2134F1 - 169
3134I1 - 169
4134L1 - 169
1144C170 - 186
2144F170 - 186
3144I170 - 186
1154C186 - 999
2154F186 - 999
3154I186 - 999
4154L186 - 999

NCS ensembles :
ID
1
2
3
4
5
DetailsThe biological unit is a trimer. There are four biological units in the asymmetric unit (chains A, B & C, chains D, E & F, chains G, H & I and chains J, K &L).

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Components

#1: Protein
Transcription elongation factor B polypeptide 2 / Elongin 18 kDa subunit / Elongin-B / EloB / RNA polymerase II transcription factor SIII subunit B / SIII p18


Mass: 11956.372 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCEB2 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370
#2: Protein
Transcription elongation factor B polypeptide 1 / Elongin 15 kDa subunit / Elongin-C / EloC / RNA polymerase II transcription factor SIII subunit C / SIII p15


Mass: 10974.616 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCEB1 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369
#3: Protein
Von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18806.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Plasmid: pHAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40337
#4: Chemical
ChemComp-3JK / (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-oxazol-5-yl)benzyl]-L-prolinamide


Mass: 399.483 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H29N3O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: PEG 3350, MgOAc, Sodium cacodylate, DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 0.993→93.901 Å / Num. all: 84490 / Num. obs: 84490 / % possible obs: 100 % / Redundancy: 12.1 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.112 / Rsym value: 0.103 / Net I/av σ(I): 4.045 / Net I/σ(I): 12.7 / Num. measured all: 1023519
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.3211.60.8180.9140759121240.260.8182.9100
2.32-2.46120.5861.3137302114750.1820.5864100
2.46-2.6312.20.411.8131533108050.1260.415.6100
2.63-2.8412.90.2712.6130938101320.0810.2718.4100
2.84-3.1112.50.1664.111630593100.050.16612.8100
3.11-3.4812.20.1135.710374385200.0350.11318100
3.48-4.0212.20.0866.89199575370.0270.08623.8100
4.02-4.9211.70.0717.77565464620.0220.07128.1100
4.92-6.96120.0677.36130950950.0210.06725.9100
6.96-49.17211.20.0517.23398130300.0170.05127.799.7

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VCB

1vcb


Resolution: 2.2→93.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.1954 / FOM work R set: 0.8173 / SU B: 12.279 / SU ML: 0.153 / SU R Cruickshank DPI: 0.2412 / SU Rfree: 0.1952 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 4270 5.1 %RANDOM
Rwork0.1967 80098 --
obs0.1988 80098 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157 Å2 / Biso mean: 51.607 Å2 / Biso min: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å2-0 Å2
3----1.05 Å2
Refinement stepCycle: final / Resolution: 2.2→93.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10517 0 116 281 10914
Biso mean--40.69 47.54 -
Num. residues----1332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910885
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210421
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.99814809
X-RAY DIFFRACTIONr_angle_other_deg0.8043.00323937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17251317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13323.22472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.088151771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6141587
X-RAY DIFFRACTIONr_chiral_restr0.0740.21695
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022425
X-RAY DIFFRACTIONr_mcbond_it2.8072.0665325
X-RAY DIFFRACTIONr_mcbond_other2.8072.0665324
X-RAY DIFFRACTIONr_mcangle_it4.3074.6266620
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1573MEDIUM POSITIONAL0.280.5
12D1573MEDIUM POSITIONAL0.240.5
13G1573MEDIUM POSITIONAL0.310.5
14J1573MEDIUM POSITIONAL0.320.5
11A1573MEDIUM THERMAL4.012
12D1573MEDIUM THERMAL7.012
13G1573MEDIUM THERMAL4.742
14J1573MEDIUM THERMAL5.252
21B1301MEDIUM POSITIONAL0.410.5
22E1301MEDIUM POSITIONAL0.420.5
23H1301MEDIUM POSITIONAL0.40.5
24K1301MEDIUM POSITIONAL0.410.5
21B1301MEDIUM THERMAL4.722
22E1301MEDIUM THERMAL4.892
23H1301MEDIUM THERMAL4.642
24K1301MEDIUM THERMAL4.952
31C1690MEDIUM POSITIONAL0.310.5
32F1690MEDIUM POSITIONAL0.370.5
33I1690MEDIUM POSITIONAL0.370.5
34L1690MEDIUM POSITIONAL0.390.5
31C1690MEDIUM THERMAL3.822
32F1690MEDIUM THERMAL4.662
33I1690MEDIUM THERMAL3.812
34L1690MEDIUM THERMAL4.762
41C241MEDIUM POSITIONAL0.30.5
42F241MEDIUM POSITIONAL0.240.5
43I241MEDIUM POSITIONAL0.380.5
41C241MEDIUM THERMAL7.62
42F241MEDIUM THERMAL3.852
43I241MEDIUM THERMAL5.92
51C228MEDIUM POSITIONAL0.30.5
52F228MEDIUM POSITIONAL0.260.5
53I228MEDIUM POSITIONAL0.320.5
54L228MEDIUM POSITIONAL0.320.5
51C228MEDIUM THERMAL6.272
52F228MEDIUM THERMAL8.582
53I228MEDIUM THERMAL6.582
54L228MEDIUM THERMAL8.642
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 310 -
Rwork0.257 5811 -
all-6121 -
obs--99.84 %
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)
12.2832-0.96010.86693.2002-1.53812.98660.03640.26870.094-0.4061-0.1833-0.14180.10810.27490.14680.12390.00210.01410.13490.02860.032745.021765.281847.6893
23.5227-0.0410.08581.7431-1.01422.2864-0.0984-0.17130.02980.108-0.0051-0.1769-0.05550.05330.10350.04890.0046-0.00450.17480.030.058448.784661.480365.3211
33.8885-0.8636-1.66891.37020.40751.58750.024-0.10210.05770.0905-0.0194-0.07680.02230.0543-0.00460.0609-0.041-0.02230.19490.07720.035527.763654.672682.5065
42.6113-0.73432.21241.6024-1.11514.9623-0.09420.72460.2061-0.2307-0.02850.0062-0.47691.13960.12270.1928-0.16160.01130.46620.01970.041748.58718.243747.4472
54.23590.52921.1560.5837-0.86083.4601-0.12140.4293-0.04290.12390.0414-0.0816-0.1710.45560.07990.1028-0.04160.00310.3216-0.02450.039353.291814.186865.2965
63.98-0.6458-1.0051.49530.43941.7067-0.03-0.0532-0.07670.09920.0455-0.11880.0164-0.0071-0.01550.0604-0.0253-0.01680.16110.04620.028732.34297.705382.2495
73.5821-0.97660.72711.2654-0.90443.3815-0.03650.3310.2167-0.1215-0.00250.0378-0.18930.220.0390.1524-0.05560.02780.29720.05510.08493.151413.083547.5256
84.3850.5770.06641.2382-0.80881.6721-0.1087-0.49320.26560.11950.0231-0.0201-0.16460.16670.08560.1433-0.01310.03070.4448-0.01650.06866.801511.272865.2635
92.8808-0.9438-1.86241.67780.18033.3041-0.0629-0.3129-0.00330.016-0.071-0.0185-0.01730.62940.13380.0117-0.0236-0.00970.34670.02090.0148-14.6097.150582.7067
102.9083-0.8395-0.56822.4121-0.64423.00570.02050.18460.0231-0.1278-0.08130.0796-0.0430.18380.06080.1107-0.0386-0.02120.130.02660.0115-0.842861.217947.7253
112.5522-0.1168-0.07211.3081-0.89712.7477-0.104-0.23620.10660.16910.0341-0.0093-0.1350.22640.06980.0917-0.0210.0030.25060.02370.03222.222459.139365.5858
122.851-0.6045-1.54361.51040.05782.7591-0.0955-0.23410.0819-0.0004-0.0059-0.00540.08570.29190.10140.0434-0.0229-0.02320.2110.05720.0378-19.017454.519982.9572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2B17 - 112
3X-RAY DIFFRACTION3C62 - 202
4X-RAY DIFFRACTION4D1 - 102
5X-RAY DIFFRACTION5E17 - 112
6X-RAY DIFFRACTION6F63 - 204
7X-RAY DIFFRACTION7G1 - 103
8X-RAY DIFFRACTION8H17 - 112
9X-RAY DIFFRACTION9I62 - 204
10X-RAY DIFFRACTION10J1 - 103
11X-RAY DIFFRACTION11K16 - 112
12X-RAY DIFFRACTION12L62 - 204

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  • 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

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