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- PDB-4w9l: pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-... -

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Basic information

Entry
Database: PDB / ID: 4w9l
TitlepVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3,3-dimethylbutanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 15)
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 / transcription elongation factor activity / target-directed miRNA degradation / 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 / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded 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 / ubiquitin-like ligase-substrate adaptor activity / Tat-mediated elongation of the HIV-1 transcript / 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 / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Vif-mediated degradation of APOBEC3G / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cell morphogenesis / Inactivation of CSF3 (G-CSF) signaling / 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 / protein-macromolecule adaptor activity / Neddylation / Replication of the SARS-CoV-2 genome / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / 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 / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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-3JJ / 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. / 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

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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)169,29216
Polymers166,94912
Non-polymers2,3434
Water4,378243
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)42,3234
Polymers41,7373
Non-polymers5861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 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)42,3234
Polymers41,7373
Non-polymers5861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-38 kcal/mol
Surface area16310 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)42,3234
Polymers41,7373
Non-polymers5861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-39 kcal/mol
Surface area16550 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)42,3234
Polymers41,7373
Non-polymers5861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-38 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.825, 93.825, 362.612
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
11F-402-

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-3JJ / N-acetyl-3-methyl-L-valyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide


Mass: 585.758 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H43N5O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.54 %
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: 0.991→93.825 Å / Num. all: 81578 / Num. obs: 81578 / % possible obs: 98.3 % / Redundancy: 6.5 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.095 / Rsym value: 0.082 / Net I/av σ(I): 6.468 / Net I/σ(I): 13.5 / Num. measured all: 533045
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
2.2-2.326.40.910.876390118800.3880.912.599.4
2.32-2.466.60.5911.274518112450.2480.5913.699.3
2.46-2.636.60.4161.768884105110.1750.4165.198.9
2.63-2.846.80.2762.46665398660.1110.2767.898.8
2.84-3.116.70.154.46028090170.0620.1512.598.5
3.11-3.486.50.0857.95355881960.0370.08518.898
3.48-4.026.40.05711.24602671920.0250.0572697.4
4.02-4.926.40.04114.13918161420.0180.04133.397.2
4.92-6.966.50.03914.53086747630.0170.03930.396.1
6.96-46.91260.02911.91668827660.0140.02934.795.1

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Processing

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

1vcb


Resolution: 2.2→93.82 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2371 / WRfactor Rwork: 0.1967 / FOM work R set: 0.8033 / SU B: 12.877 / SU ML: 0.161 / SU R Cruickshank DPI: 0.262 / SU Rfree: 0.2061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.243 4128 5.1 %RANDOM
Rwork0.2038 77450 --
obs0.2058 77450 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.64 Å2 / Biso mean: 49.505 Å2 / Biso min: 20.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-0 Å2-0 Å2
2--0.32 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 2.2→93.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10524 0 164 243 10931
Biso mean--41.15 44.28 -
Num. residues----1331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910940
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210491
X-RAY DIFFRACTIONr_angle_refined_deg1.2842.00114891
X-RAY DIFFRACTIONr_angle_other_deg0.7743.00524090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04751315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43223.27474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.701151777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0541586
X-RAY DIFFRACTIONr_chiral_restr0.0690.21706
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112084
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022434
X-RAY DIFFRACTIONr_mcbond_it1.9451.6255320
X-RAY DIFFRACTIONr_mcbond_other1.9441.6255319
X-RAY DIFFRACTIONr_mcangle_it3.1733.6346612
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1583MEDIUM POSITIONAL0.280.5
12D1583MEDIUM POSITIONAL0.210.5
13G1583MEDIUM POSITIONAL0.230.5
14J1583MEDIUM POSITIONAL0.30.5
11A1583MEDIUM THERMAL4.562
12D1583MEDIUM THERMAL5.542
13G1583MEDIUM THERMAL4.052
14J1583MEDIUM THERMAL3.762
21B1337MEDIUM POSITIONAL0.370.5
22E1337MEDIUM POSITIONAL0.40.5
23H1337MEDIUM POSITIONAL0.360.5
24K1337MEDIUM POSITIONAL0.340.5
21B1337MEDIUM THERMAL4.432
22E1337MEDIUM THERMAL4.22
23H1337MEDIUM THERMAL4.922
24K1337MEDIUM THERMAL4.042
31C1690MEDIUM POSITIONAL0.30.5
32F1690MEDIUM POSITIONAL0.360.5
33I1690MEDIUM POSITIONAL0.390.5
34L1690MEDIUM POSITIONAL0.40.5
31C1690MEDIUM THERMAL5.332
32F1690MEDIUM THERMAL7.252
33I1690MEDIUM THERMAL5.632
34L1690MEDIUM THERMAL6.892
41C225MEDIUM POSITIONAL0.180.5
42F225MEDIUM POSITIONAL0.130.5
43I225MEDIUM POSITIONAL0.210.5
41C225MEDIUM THERMAL6.412
42F225MEDIUM THERMAL2.962
43I225MEDIUM THERMAL6.432
51C244MEDIUM POSITIONAL0.570.5
52F244MEDIUM POSITIONAL0.380.5
53I244MEDIUM POSITIONAL0.340.5
54L244MEDIUM POSITIONAL0.340.5
51C244MEDIUM THERMAL5.922
52F244MEDIUM THERMAL9.212
53I244MEDIUM THERMAL5.892
54L244MEDIUM THERMAL8.452
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 302 -
Rwork0.288 5705 -
all-6007 -
obs--98.98 %
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)
12.3572-0.78010.63972.637-1.40173.13210.03790.2635-0.003-0.2709-0.1779-0.08460.01210.26590.140.17980.00230.00710.18060.0030.110144.474665.654547.1562
23.790.03640.19280.7271-0.49982.9405-0.0385-0.1325-0.01890.0482-0.0453-0.0612-0.0620.0750.08380.08140.00860.00380.18970.04040.112248.367461.667464.7369
34.6668-0.8365-1.72271.62950.07311.62640.0301-0.18850.05310.0946-0.0331-0.0914-0.04330.05760.0030.0149-0.026-0.0260.18460.0740.063627.325454.791881.7514
42.4396-0.46351.70172.4478-1.20414.6198-0.02950.64290.2467-0.22-0.1333-0.0858-0.33220.89460.16280.2577-0.07150.02720.38220.02950.113948.062218.97346.9551
54.3850.41671.35970.2425-0.69013.7435-0.06290.23130.02010.0293-0.0496-0.0237-0.19310.41140.11240.1867-0.00830.03190.30.01910.120952.92614.735664.765
63.764-1.0214-0.89942.22640.43351.44880.0069-0.1612-0.00090.0729-0.0391-0.0434-0.0078-0.16550.03220.0308-0.0378-0.03670.21560.0470.045632.10377.722681.3826
73.7146-1.75410.16471.4268-0.85134.08970.04510.37660.2838-0.2223-0.08010.0169-0.17840.28070.0350.3121-0.05410.03180.51440.05090.24142.650613.570447.0768
85.6447-0.327-1.01261.2614-0.48671.4191-0.1447-0.38240.28710.08840.1139-0.1061-0.1890.24080.03070.2580.02050.02290.6295-0.020.22296.462211.749564.8167
93.0283-0.7035-1.09491.8876-0.19593.75320.0023-0.1542-0.00880.0647-0.0784-0.10010.20410.69660.07620.10860.0139-0.00330.32720.02790.1689-15.23017.592682.119
102.7857-0.6854-0.48022.109-0.63053.26590.00340.20120.0985-0.1281-0.07160.0283-0.1440.28090.06820.1621-0.0345-0.01310.26850.0510.1384-1.28661.648647.2354
113.9587-0.1341-0.51291.1683-0.42892.8192-0.1104-0.28580.17640.1020.0337-0.0444-0.07890.40130.07670.15290.00210.01310.35410.02220.14031.739459.416664.9965
122.1506-0.3602-1.72781.3787-0.04883.2994-0.069-0.24270.0154-0.025-0.0723-0.00960.13380.44710.14130.08010.0045-0.01370.25750.06640.1248-19.736254.593982.1727
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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