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- PDB-4ibs: Human p53 core domain with hot spot mutation R273H (form I) -

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Basic information

Entry
Database: PDB / ID: 4ibs
TitleHuman p53 core domain with hot spot mutation R273H (form I)
ComponentsCellular tumor antigen p53
KeywordsDNA BINDING PROTEIN / METAL-BINDING / LOOP-SHEET-HELIX MOTIF / TRANSCRIPTION / ACTIVATOR / ANTI-ONCOGENE / APOPTOSIS / CELL CYCLE / DISEASE MUTATION / RESCUE MUTATION / TUMOR SUPPRESSOR
Function / homology
Function and homology information


Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / T cell lineage commitment / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / B cell lineage commitment / thymocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / T cell proliferation involved in immune response / negative regulation of reactive oxygen species metabolic process / positive regulation of execution phase of apoptosis / Transcriptional Regulation by VENTX / replicative senescence / cellular response to UV-C / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to actinomycin D / neuroblast proliferation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / type II interferon-mediated signaling pathway / hematopoietic stem cell differentiation / Pyroptosis / chromosome organization / viral process / embryonic organ development / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / mitophagy / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / positive regulation of intrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / negative regulation of proteolysis / Regulation of TP53 Activity through Acetylation / mitotic G1 DNA damage checkpoint signaling / gastrulation / 14-3-3 protein binding / response to salt stress / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription repressor complex
Similarity search - Function
Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain ...Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsRozenberg, H. / Eldar, A. / Diskin-Posner, Y. / Shakked, Z.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions.
Authors: Eldar, A. / Rozenberg, H. / Diskin-Posner, Y. / Rohs, R. / Shakked, Z.
History
DepositionDec 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2709
Polymers89,9464
Non-polymers3245
Water11,692649
1
A: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5522
Polymers22,4871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5522
Polymers22,4871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5522
Polymers22,4871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6143
Polymers22,4871
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.852, 70.179, 83.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cellular tumor antigen p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 22486.535 Da / Num. of mol.: 4 / Fragment: DNA binding domain / Mutation: R273H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P53, TP53 / Plasmid: pET-27-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04637
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 12% PEG 3350, 0.12M Mg-Formate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2005 / Details: BLUE CONFOCAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.36
ReflectionResolution: 1.78→32 Å / Num. obs: 74257 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.059 / Χ2: 1.083 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.78-1.815.90.33531780.864183.1
1.81-1.846.20.30833930.907189.8
1.84-1.886.60.27635610.948194.6
1.88-1.926.90.23836671.011196
1.92-1.967.20.21337001.049196.9
1.96-27.40.18637311.081197.4
2-2.057.50.1636871.11197.4
2.05-2.117.50.13837001.154197.5
2.11-2.177.50.12537371.197197.8
2.17-2.247.50.10737361.187198.1
2.24-2.327.50.09937621.177198.4
2.32-2.427.50.09337601.163198.6
2.42-2.537.50.08437941.165198.8
2.53-2.667.50.07337751.116198.9
2.66-2.837.60.06137761.09199.4
2.83-3.047.60.05138071.043199.5
3.04-3.357.60.04338481.025199.7
3.35-3.837.60.03538421.098199.9
3.83-4.837.60.03238531.0411100
4.83-327.50.03439501.073199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_1218refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TSR

1tsr


Resolution: 1.78→25.05 Å / Occupancy max: 1 / Occupancy min: 0.06 / FOM work R set: 0.8399 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.43 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 2564 3.45 %RANDOM
Rwork0.1633 ---
obs0.1642 74239 97.06 %-
all-74239 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.39 Å2 / Biso mean: 21.0129 Å2 / Biso min: 7.55 Å2
Refinement stepCycle: LAST / Resolution: 1.78→25.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5985 0 8 649 6642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046538
X-RAY DIFFRACTIONf_angle_d0.8778966
X-RAY DIFFRACTIONf_chiral_restr0.058981
X-RAY DIFFRACTIONf_plane_restr0.0041216
X-RAY DIFFRACTIONf_dihedral_angle_d13.7962477
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.81470.32631250.29223408353380
1.8147-1.85170.24811230.25563698382188
1.8517-1.89190.21671370.22093868400592
1.8919-1.93590.20721450.1963931407693
1.9359-1.98420.18861370.18943952408994
1.9842-2.03780.17451390.18393979411894
2.0378-2.09770.22441440.18283973411794
2.0977-2.16540.19551360.17693988412495
2.1654-2.24260.19511500.17614010416095
2.2426-2.33230.15111410.16584035417695
2.3323-2.43820.22091360.16944065420195
2.4382-2.56650.20421450.1674019416495
2.5665-2.72690.16311390.1634085422496
2.7269-2.93680.17151400.15964072421296
2.9368-3.23110.18221470.15944112425996
3.2311-3.69580.15661450.14754127427296
3.6958-4.64570.1541480.12034149429797
4.6457-19.34980.16481490.1454199434897
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)
10.4447-0.293-0.04120.127-0.01960.2334-0.006-0.0548-0.03170.00890.0487-0.0461-0.02220.10330.0440.06940.0062-0.01160.10280.0060.096634.9741.0812-28.8459
20.2377-0.1098-0.16750.1647-0.01380.24790.02290.020.07360.02080.05320.0056-0.1961-0.29750.02790.13630.03680.00030.12890.01240.123523.004311.7809-35.9882
30.362-0.22050.32290.2773-0.07220.29850.02620.03140.0667-0.0225-0.0287-0.0613-0.1115-0.0037-0.02970.1302-0.00380.00560.1021-0.00460.123133.51276.2939-32.4352
40.3217-0.0249-0.36020.06880.00530.4349-0.0065-0.14770.0934-0.0045-0.01470.0854-0.06520.1444-0.03110.118-0.0291-0.0350.0687-0.02770.153234.76719.965419.9768
50.5592-0.0735-0.093-0.02730.10050.07640.012-0.00230.0275-00.0088-0.0528-0.02860.01110.02840.09580.00530.00970.09460.00390.12936.76211.8999.2261
61.67870.2710.00020.0511-0.00430.15670.28230.62070.6025-0.0487-0.25650.0576-0.0894-0.14280.10810.09160.0382-0.03780.27620.05160.077622.57658.7175-1.3974
70.58130.0535-0.33480.34450.31331.0381-0.06960.22670.0610.160.0188-0.04450.3927-0.3127-0.0033-0.0332-0.0191-0.00230.089-0.01620.10919.95040.34086.7059
80.09710.0599-0.00820.04410.05140.15380.02250.0005-0.0657-0.1005-0.0574-0.01920.1785-0.0337-0.0410.10560.0157-0.00710.08190.02460.135231.2012-5.283419.5813
90.6127-0.13650.01070.09870.04830.1085-0.02760.08980.0887-0.0171-0.0142-0.0491-0.0491-0.0263-0.04780.10980.0037-0.00340.07860.01360.13231.20325.12617.349
100.1364-0.04560.00040.03130.00250.011-0.03050.1564-0.033-0.14820.02590.076-0.1710.13530.00760.12680.0122-0.00930.17970.04150.09348.23684.2348-3.0893
110.6921-0.09460.07220.03230.11240.03890.02060.0364-0.04610.0359-0.01090.00670.0060.0159-0.01090.09490.00060.01290.13880.00010.144172.4825-3.61526.0749
120.2650.00110.01990.06330.12720.86480.0489-0.1825-0.17340.00270.0432-0.01270.0661-0.35170.04190.1063-0.0297-0.01550.14670.05750.160159.7815-10.895416.5247
130.5956-0.31780.16730.1664-0.01920.1026-0.0593-0.0395-0.01110.01940.002-0.0129-0.1386-0.0339-0.06050.0808-0.0053-0.00060.08370.00680.100758.15340.26028.169
140.63790.093-0.01550.07740.23630.3824-0.0317-0.1302-0.09520.0615-0.0085-0.00930.0226-0.0073-0.05840.0968-0.0004-0.00050.14140.02420.118668.9985-6.465513.2796
150.62970.03190.14790.29880.29480.88790.16350.0675-0.05420.17790.2814-0.05280.16790.26360.3783-0.04890.07540.05140.43080.03090.141263.9062-9.48-46.0704
160.22840.16650.06490.0616-0.00770.045-0.00080.05350.01090.00810.0004-0.105-0.0512-0.0780.01410.0753-0.0039-0.00210.2311-0.00850.115772.5237-1.3894-29.7093
170.14030.0358-0.02930.0480.05410.0824-0.03550.19450.017-0.04090.0459-0.14450.01670.05790.00190.1022-0.02260.00930.24570.02890.154960.3442-2.1755-42.6898
180.1220.0896-0.06150.0372-0.02190.10910.0423-0.3582-0.25560.01210.05470.1454-0.0179-0.00740.02440.0999-0.0130.0070.24010.03960.156454.5885-9.7402-23.8507
190.81740.030.1040.21110.10960.2298-0.0047-0.0276-0.0222-0.0177-0.0412-0.00330.020.0779-0.02950.0843-0.0062-0.01060.18160.00480.102558.0278-3.2455-33.9211
200.19580.07760.0790.12780.04740.18280.0373-0.126-0.2292-0.01870.0241-0.0768-0.0218-0.2632-0.01930.0876-0.023-0.0030.22030.02390.164872.6434-8.9866-29.0029
210.21110.1145-0.04450.0347-0.02410.0958-0.02740.16970.018-0.0155-0.07170.01040.04-0.2414-0.0030.0861-0.00620.0050.146-0.01740.117417.03281.2177-35.0902
220.4120.0352-0.05770.28030.29460.2574-0.02880.0141-0.0954-0.08850.03890.03320.0255-0.0455-0.00630.11680.0067-0.00310.09210.00760.128628.20970.2957-33.3995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 96:155 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 156:180 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 251:288 )A0
4X-RAY DIFFRACTION4CHAIN B AND (RESID 96:112 )B0
5X-RAY DIFFRACTION5CHAIN B AND (RESID 113:168 )B0
6X-RAY DIFFRACTION6CHAIN B AND (RESID 169:180 )B0
7X-RAY DIFFRACTION7CHAIN B AND (RESID 181:213 )B0
8X-RAY DIFFRACTION8CHAIN B AND (RESID 214:229 )B0
9X-RAY DIFFRACTION9CHAIN B AND (RESID 230:277 )B0
10X-RAY DIFFRACTION10CHAIN B AND (RESID 278:289 )B0
11X-RAY DIFFRACTION11CHAIN C AND (RESID 96:155 )C0
12X-RAY DIFFRACTION12CHAIN C AND (RESID 156:181 )C0
13X-RAY DIFFRACTION13CHAIN C AND (RESID 182:229 )C0
14X-RAY DIFFRACTION14CHAIN C AND (RESID 230:289 )C0
15X-RAY DIFFRACTION15CHAIN D AND (RESID 96:109 )D0
16X-RAY DIFFRACTION16CHAIN D AND (RESID 110:146 )D0
17X-RAY DIFFRACTION17CHAIN D AND (RESID 147:163 )D0
18X-RAY DIFFRACTION18CHAIN D AND (RESID 164:194 )D0
19X-RAY DIFFRACTION19CHAIN D AND (RESID 195:263 )D0
20X-RAY DIFFRACTION20CHAIN D AND (RESID 264:289 )D0
21X-RAY DIFFRACTION21CHAIN A AND (RESID 181:213)A0
22X-RAY DIFFRACTION22CHAIN A AND (RESID 214:250)A0

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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

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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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