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- PDB-4w9h: pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamido-3,3-dim... -

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Basic information

Entry
Database: PDB / ID: 4w9h
TitlepVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 7)
Components
  • (Transcription elongation factor B polypeptide ...) x 3
  • Von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / protein complex / ubiquitin ligase / hypoxia inducible factor
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 initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / cell morphogenesis / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / 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 / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / protein-macromolecule adaptor activity / 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 / 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 / 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-3JF / 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
AuthorsGadd, M.S. / Soares, P. / 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 / 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)169,04716
Polymers167,15712
Non-polymers1,8904
Water10,359575
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)42,3144
Polymers41,8413
Non-polymers4731
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-39 kcal/mol
Surface area15910 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)42,3144
Polymers41,8413
Non-polymers4731
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-40 kcal/mol
Surface area16060 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)42,2104
Polymers41,7373
Non-polymers4731
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-38 kcal/mol
Surface area16290 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)42,2104
Polymers41,7373
Non-polymers4731
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-38 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.980, 92.980, 364.372
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

21G-210-

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

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Transcription elongation factor B polypeptide ... , 3 types, 8 molecules ADGJBEHK

#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: 11078.599 Da / Num. of mol.: 2
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
#4: 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.: 2
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

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Protein , 1 types, 4 molecules CFIL

#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

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Non-polymers , 2 types, 579 molecules

#5: Chemical
ChemComp-3JF / N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide


Mass: 472.600 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H32N4O4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 0.991→93.1 Å / Num. all: 94556 / Num. obs: 94556 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.124 / Rsym value: 0.104 / Net I/av σ(I): 5.727 / Net I/σ(I): 9.6 / Num. measured all: 613573
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
2.1-2.216.60.8310.989745136010.380.8312100
2.21-2.356.60.5861.384387128320.2690.5862.8100
2.35-2.516.80.4271.882022121400.1930.4273.8100
2.51-2.716.60.2762.874414112810.1270.2765.499.9
2.71-2.976.50.1724.468430104880.0790.1728.2100
2.97-3.326.50.1066.86139595030.0490.10612.899.8
3.32-3.836.40.0729.25392784280.0340.07218.499.8
3.83-4.76.20.05410.34446672070.0260.0542499.8
4.7-6.646.20.0510.53565457210.0240.0522100
6.64-48.8165.70.03212.61913333550.0170.03223.299.6

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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: 2.1→93.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2395 / WRfactor Rwork: 0.1971 / FOM work R set: 0.784 / SU B: 12.107 / SU ML: 0.162 / SU R Cruickshank DPI: 0.2255 / SU Rfree: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 4784 5.1 %RANDOM
Rwork0.2097 89653 --
obs0.212 89653 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.86 Å2 / Biso mean: 40.519 Å2 / Biso min: 18.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 2.1→93.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10558 0 132 575 11265
Biso mean--31.24 40.77 -
Num. residues----1332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910943
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210483
X-RAY DIFFRACTIONr_angle_refined_deg1.336214887
X-RAY DIFFRACTIONr_angle_other_deg0.7563.00424080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28451317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33823.271480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.878151783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8841588
X-RAY DIFFRACTIONr_chiral_restr0.070.21702
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022442
X-RAY DIFFRACTIONr_mcbond_it1.9351.6495325
X-RAY DIFFRACTIONr_mcbond_other1.9341.6495324
X-RAY DIFFRACTIONr_mcangle_it3.1253.6956620
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1573MEDIUM POSITIONAL0.330.5
12D1573MEDIUM POSITIONAL0.280.5
13G1573MEDIUM POSITIONAL0.360.5
14J1573MEDIUM POSITIONAL0.290.5
11A1573MEDIUM THERMAL3.012
12D1573MEDIUM THERMAL3.382
13G1573MEDIUM THERMAL3.682
14J1573MEDIUM THERMAL3.852
21B1314MEDIUM POSITIONAL0.450.5
22E1314MEDIUM POSITIONAL0.530.5
23H1314MEDIUM POSITIONAL0.610.5
24K1314MEDIUM POSITIONAL0.470.5
21B1314MEDIUM THERMAL5.32
22E1314MEDIUM THERMAL4.782
23H1314MEDIUM THERMAL6.322
24K1314MEDIUM THERMAL4.382
31C1690MEDIUM POSITIONAL0.370.5
32F1690MEDIUM POSITIONAL0.460.5
33I1690MEDIUM POSITIONAL0.40.5
34L1690MEDIUM POSITIONAL0.40.5
31C1690MEDIUM THERMAL3.392
32F1690MEDIUM THERMAL3.372
33I1690MEDIUM THERMAL3.412
34L1690MEDIUM THERMAL3.522
41C241MEDIUM POSITIONAL0.270.5
42F241MEDIUM POSITIONAL0.210.5
43I241MEDIUM POSITIONAL0.40.5
41C241MEDIUM THERMAL7.012
42F241MEDIUM THERMAL2.782
43I241MEDIUM THERMAL7.482
51C255MEDIUM POSITIONAL0.30.5
52F255MEDIUM POSITIONAL0.310.5
53I255MEDIUM POSITIONAL0.340.5
54L255MEDIUM POSITIONAL0.330.5
51C255MEDIUM THERMAL5.382
52F255MEDIUM THERMAL6.842
53I255MEDIUM THERMAL7.052
54L255MEDIUM THERMAL4.992
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 358 -
Rwork0.293 6492 -
all-6850 -
obs--99.77 %
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)
11.3597-0.62790.62862.4261-1.14441.87820.01380.16690.0435-0.3259-0.1646-0.1760.05170.26140.15080.10910.0120.02240.12760.02170.016744.586864.645747.4208
22.7273-0.58640.93860.1711-0.26651.2485-0.1495-0.34870.05550.09840.0404-0.0672-0.0915-0.03970.10910.1560.0163-0.04160.21630.06180.109148.262860.982465.0055
33.3534-0.8685-1.83361.02310.49081.3609-0.0656-0.00210.04290.1027-0.0071-0.05860.03720.07910.07280.0707-0.0547-0.01780.17210.05270.035927.393454.330882.2649
41.9575-0.46191.51980.8353-1.03813.4411-0.0690.42010.2077-0.1387-0.08320.0194-0.37450.82790.15220.209-0.1284-0.02570.34590.04930.044948.049217.991347.1851
51.7299-0.10451.16320.0764-0.34861.9388-0.10020.32150.00990.0593-0.0292-0.0248-0.21980.32610.12940.1434-0.03080.01220.3372-0.00360.048552.614714.041664.9324
63.6186-0.6026-0.87831.0290.42951.5558-0.064-0.0184-0.04440.10.0081-0.0736-0.0010.00980.05590.048-0.026-0.01230.11050.02770.018931.69917.681181.835
72.355-0.48530.58261.2182-0.71822.41680.02140.28020.2087-0.0509-0.06740.0747-0.20760.17440.0460.1104-0.01750.0140.20650.03650.04073.047812.93347.3565
82.93890.14360.47481.2297-0.70311.6012-0.1027-0.29090.23490.1314-0.0231-0.0528-0.22620.11090.12580.1271-0.02730.00340.2949-0.01970.03096.656210.959565.0911
92.1585-0.6403-0.45151.16380.19261.3043-0.0649-0.16430.04060.0180.00850.0278-0.05660.2050.05640.0476-0.0348-0.00650.27960.00730.0057-14.55066.927882.2414
101.9977-0.707-0.32611.7866-0.37231.9196-0.00490.13520.0198-0.0575-0.0510.0547-0.01450.0980.05590.0844-0.0084-0.00540.0880.00870.0064-0.919760.637247.6103
112.3082-0.83710.36581.3326-0.81831.9864-0.0737-0.21870.02360.085-0.0199-0.021-0.15060.15280.09360.074-0.0138-0.00060.1870.00640.00562.219258.495965.3531
122.4209-0.293-1.83271.15730.04643.2533-0.1227-0.31620.0683-0.01960.02510.0340.02740.33460.09760.0227-0.0174-0.020.17850.03210.0257-18.884453.958182.5638
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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Major update of PDB

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  • 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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