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- PDB-4w9f: pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4... -

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Basic information

Entry
Database: PDB / ID: 4w9f
TitlepVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 5)
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 / Replication of the SARS-CoV-1 genome / VCB complex / 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 / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / SUMOylation of ubiquitinylation proteins / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / 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 / protein serine/threonine kinase binding / 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 / 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 / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / microtubule cytoskeleton / regulation of gene expression / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / cellular response to hypoxia / molecular adaptor activity / DNA-binding transcription factor binding / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / cilium / 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 / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / 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-C / Elongin B / 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-3JU / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsvan Molle, I. / Hewitt, S. / Galdeano, C. / Gadd, M.S. / Ciulli, A.
Funding support United Kingdom, 4items
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
Marie Sklodowska-Curie ActionsEC PIEF-GA-2010-275683
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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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)168,61116
Polymers166,94912
Non-polymers1,6624
Water10,809600
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)42,1534
Polymers41,7373
Non-polymers4161
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-38 kcal/mol
Surface area15700 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)42,1534
Polymers41,7373
Non-polymers4161
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-34 kcal/mol
Surface area15490 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)42,1534
Polymers41,7373
Non-polymers4161
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-39 kcal/mol
Surface area15970 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)42,1534
Polymers41,7373
Non-polymers4161
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-35 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.680, 92.680, 364.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
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: 11852.389 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: 11078.599 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-3JU / (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide


Mass: 415.549 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H29N3O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
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: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→92.68 Å / Num. obs: 93841
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.1513.40.851.3032.6691870685668561.355100
2.15-2.210.9151.0413.585385663766371.084100
2.21-2.280.9340.8464.3488429647764760.879100
2.28-2.350.9570.6725.485382629762970.698100
2.35-2.420.9730.5596.3181039610661060.581100
2.42-2.510.980.4497.6176521591959190.467100
2.51-2.60.990.3479.4777051569856970.361100
2.6-2.710.9920.27211.5470980551155110.283100
2.71-2.830.9950.20714.671743531453140.215100
2.83-2.970.9970.14519.3468429508350830.151100
2.97-3.130.9980.11223.2762315483248320.116100
3.13-3.320.9990.08828.3760586460846070.091100
3.32-3.550.9980.07133.5355435434343420.074100
3.55-3.830.9990.05837.7951226404540450.061100
3.83-4.20.9990.05142.7647314374337420.054100
4.2-4.70.9970.04845.0640439342134200.05100
4.7-5.420.9990.04744.6536353303830380.049100
5.42-6.6410.0540.9330987261526150.052100
6.64-9.390.9970.04344.1823139208020760.04599.8
9.390.9990.03845.5512868124412280.0498.7

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Processing

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

1vbc


Resolution: 2.1→92.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2277 / WRfactor Rwork: 0.204 / FOM work R set: 0.8094 / SU B: 10.383 / SU ML: 0.14 / SU R Cruickshank DPI: 0.2146 / SU Rfree: 0.1715 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 4704 5 %RANDOM
Rwork0.2047 89136 --
obs0.206 89136 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.78 Å2 / Biso mean: 43.74 Å2 / Biso min: 25.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0 Å2
2--0.41 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 2.1→92.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10174 0 116 603 10893
Biso mean--37.29 47.5 -
Num. residues----1317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01910579
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210029
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.99514425
X-RAY DIFFRACTIONr_angle_other_deg0.7453.00422978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95451305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06323.115427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.669151639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6661574
X-RAY DIFFRACTIONr_chiral_restr0.0630.21676
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022352
X-RAY DIFFRACTIONr_mcbond_it1.9131.8535279
X-RAY DIFFRACTIONr_mcbond_other1.9141.8535278
X-RAY DIFFRACTIONr_mcangle_it3.1534.1466564
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1362MEDIUM POSITIONAL0.320.5
12D1362MEDIUM POSITIONAL0.430.5
13G1362MEDIUM POSITIONAL0.320.5
14J1362MEDIUM POSITIONAL0.380.5
11A1362MEDIUM THERMAL5.412
12D1362MEDIUM THERMAL5.952
13G1362MEDIUM THERMAL7.612
14J1362MEDIUM THERMAL6.622
21B1226MEDIUM POSITIONAL0.460.5
22E1226MEDIUM POSITIONAL0.530.5
23H1226MEDIUM POSITIONAL0.570.5
24K1226MEDIUM POSITIONAL0.470.5
21B1226MEDIUM THERMAL3.622
22E1226MEDIUM THERMAL4.012
23H1226MEDIUM THERMAL3.852
24K1226MEDIUM THERMAL5.812
31C1579MEDIUM POSITIONAL0.320.5
32F1579MEDIUM POSITIONAL0.370.5
33I1579MEDIUM POSITIONAL0.370.5
34L1579MEDIUM POSITIONAL0.350.5
31C1579MEDIUM THERMAL3.092
32F1579MEDIUM THERMAL2.742
33I1579MEDIUM THERMAL3.152
34L1579MEDIUM THERMAL4.52
41C218MEDIUM POSITIONAL0.320.5
42F218MEDIUM POSITIONAL0.230.5
43I218MEDIUM POSITIONAL0.330.5
41C218MEDIUM THERMAL4.012
42F218MEDIUM THERMAL2.752
43I218MEDIUM THERMAL3.852
51C207MEDIUM POSITIONAL0.680.5
52F207MEDIUM POSITIONAL0.460.5
53I207MEDIUM POSITIONAL0.380.5
54L207MEDIUM POSITIONAL0.40.5
51C207MEDIUM THERMAL8.952
52F207MEDIUM THERMAL6.162
53I207MEDIUM THERMAL5.442
54L207MEDIUM THERMAL9.252
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 344 -
Rwork0.269 6510 -
all-6854 -
obs--99.99 %
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)
11.1281-0.7389-0.86650.61180.82431.2568-0.0484-0.091-0.01330.0534-0.00280.01920.1180.0150.05120.149-0.01790.05920.10440.02670.2148-18.25592.454843.3937
20.198-0.1406-0.46840.50070.25971.22630.02170.0517-0.0624-0.0487-0.0837-0.0167-0.027-0.06560.06190.18680.01110.03610.0596-0.01140.2452-14.2408-1.559325.9024
30.4887-0.5650.23641.7927-1.03920.6532-0.01830.0983-0.05230.0434-0.03530.03240.0251-0.00670.05360.2143-0.04290.05590.0613-0.00420.1947-7.96819.93689.1306
40.6511-0.6259-0.76620.78571.20872.28020.0229-0.08260.11490.1479-0.042-0.01960.571-0.27470.01910.316-0.1690.03360.150.00410.158228.3941-1.020843.4492
50.3336-0.596-0.2941.18040.32242.5092-0.02180.0343-0.00240.1757-0.0084-0.00090.3269-0.1970.03020.3183-0.0321-0.01130.06110.01550.195332.4762-5.777426.1417
60.49-0.53950.34211.845-0.47890.47540.02310.0784-0.05170.0357-0.0342-0.02080.013-0.04040.01110.1749-0.03070.03270.0645-0.00490.211638.499315.18889.2733
70.4854-0.483-0.69690.74040.25512.0941-0.11590.0130.04450.16520.03680.01620.1024-0.1140.07910.2235-0.020.03430.07110.01040.190833.427843.318443.4626
80.0507-0.0561-0.23550.81960.39281.135-0.01750.0264-0.0101-0.1925-0.06880.0120.0933-0.13370.08630.273-0.0192-0.00670.04770.02330.198435.185540.15326.0148
90.4244-0.41990.03750.9315-0.1050.3957-0.0368-0.03360.0179-0.1843-0.03690.02620.0939-0.01280.07360.3784-0.007-0.00870.0186-0.00060.166839.349460.85178.9182
100.8749-0.6143-0.36690.6339-0.01260.9161-0.017-0.0740.07580.0057-0.01360.01340.1107-0.00040.03060.1435-0.04630.03340.097-0.00960.2159-14.462547.563743.3858
110.0985-0.21-0.18021.1525-0.31941.1780.02530.0216-0.0013-0.2505-0.07740.04580.1894-0.08240.05210.2362-0.0230.02250.06680.00740.2127-12.219744.613125.6862
120.5178-0.3301-0.03151.0769-1.03851.6953-0.0154-0.03510.0428-0.1829-0.06530.02320.2215-0.03990.08070.25640.00060.02040.0755-0.0310.2044-8.357767.48378.5035
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 - 203
7X-RAY DIFFRACTION7G1 - 103
8X-RAY DIFFRACTION8H17 - 110
9X-RAY DIFFRACTION9I62 - 204
10X-RAY DIFFRACTION10J1 - 103
11X-RAY DIFFRACTION11K16 - 112
12X-RAY DIFFRACTION12L62 - 204

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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

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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

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