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- PDB-4ibz: Human p53 core domain with hot spot mutation R273C and second-sit... -

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Basic information

Entry
Database: PDB / ID: 4ibz
TitleHuman p53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R
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 / 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 / Activation of NOXA and translocation to mitochondria / 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 / 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 / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / T cell lineage commitment / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / B cell lineage commitment / thymocyte apoptotic process / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / ER overload response / positive regulation of release of cytochrome c from mitochondria / negative regulation of DNA replication / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / Zygotic genome activation (ZGA) / positive regulation of execution phase of apoptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / Pyroptosis / mitophagy / cellular response to UV-C / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / somitogenesis / embryonic organ development / chromosome organization / T cell proliferation involved in immune response / type II interferon-mediated signaling pathway / glial cell proliferation / viral process / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / cellular response to actinomycin D / positive regulation of intrinsic apoptotic signaling pathway / cellular response to glucose starvation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / mitotic G1 DNA damage checkpoint signaling / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / tumor necrosis factor-mediated signaling pathway / response to salt stress / cardiac muscle cell apoptotic process / 14-3-3 protein binding / Regulation of TP53 Activity through Acetylation
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
ACETATE ION / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsEldar, A. / Rozenberg, H. / 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)91,59029
Polymers90,0304
Non-polymers1,55925
Water11,043613
1
A: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8216
Polymers22,5081
Non-polymers3145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9428
Polymers22,5081
Non-polymers4357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8216
Polymers22,5081
Non-polymers3145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0049
Polymers22,5081
Non-polymers4978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.742, 70.413, 84.585
Angle α, β, γ (deg.)90.000, 89.920, 90.000
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: 22507.621 Da / Num. of mol.: 4 / Fragment: DNA binding domain / Mutation: R273C, T284R
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.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 12% PEG 3350, 0.12M NH4-Acetate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9759 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 5, 2005 / Details: TOROIDAL MIRROR
RadiationMonochromator: SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9759 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.07
ReflectionResolution: 1.92→27 Å / Num. obs: 60012 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.081 / Χ2: 1.084 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.92-1.952.60.35625010.9181.2
1.95-1.992.90.35829010.911196.3
1.99-2.0330.32430070.951198.1
2.03-2.073.40.27629930.995198.3
2.07-2.113.90.27130081.036198.5
2.11-2.163.90.2529791.066198.3
2.16-2.223.90.20230101.111198.2
2.22-2.283.90.1830421.179198.8
2.28-2.343.90.16930161.166198.8
2.34-2.423.90.14129901.101198.5
2.42-2.513.90.13230391.137199.1
2.51-2.613.90.11430291.093199
2.61-2.723.90.10130201.178199
2.72-2.873.90.08930471.15199.2
2.87-3.053.80.07730381.139199.2
3.05-3.283.80.06630641.079199.4
3.28-3.613.80.05930521.052199.3
3.61-4.133.70.05530591.084198.9
4.13-5.23.70.05130971.055199.4
5.2-273.60.04831201.078198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ACO, chain A
Resolution: 1.92→26.692 Å / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.7844 / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 28.39 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 2544 4.24 %RANDOM
Rwork0.1792 ---
obs0.1807 59996 97.44 %-
all-59996 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.15 Å2 / Biso mean: 33.0886 Å2 / Biso min: 5.7 Å2
Refinement stepCycle: LAST / Resolution: 1.92→26.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5922 0 88 613 6623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076448
X-RAY DIFFRACTIONf_angle_d1.0698774
X-RAY DIFFRACTIONf_chiral_restr0.07949
X-RAY DIFFRACTIONf_plane_restr0.0051182
X-RAY DIFFRACTIONf_dihedral_angle_d14.5752444
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 (%)
1.92-1.96020.3133900.28812580267075
1.9602-2.00020.30971550.26493146330192
2.0002-2.04370.27821340.25033143327794
2.0437-2.09110.31691360.2293222335894
2.0911-2.14340.3041460.23993203334994
2.1434-2.20120.23511340.23013232336695
2.2012-2.26590.27851320.21863179331195
2.2659-2.33890.30161490.22133221337094
2.3389-2.42230.29311380.22063196333494
2.4223-2.51910.26411360.22193243337995
2.5191-2.63350.22871430.21393212335595
2.6335-2.77190.25461320.20493255338795
2.7719-2.9450.23041420.19393245338795
2.945-3.17140.24441420.17083261340395
3.1714-3.48870.20171400.15243255339595
3.4887-3.98940.21651380.12923245338395
3.9894-5.01070.21500.11323305345595
5.0107-18.89740.16121480.14393316346495
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.42941.67581.3155.84734.06645.6798-0.13290.53510.48040.0050.0926-0.0242-0.57990.0880.07730.2646-0.0161-0.030.13960.02960.2049-29.3524-8.3387-22.9787
22.4461-0.3648-0.12321.33280.00411.4278-0.0179-0.1016-0.03380.11620.06430.0447-0.14040.026-0.01010.1932-0.00360.02330.064-0.0060.1815-31.0783-12.5812-8.6047
33.76430.97320.55113.16511.24993.1843-0.0633-0.2144-0.20620.10140.0162-0.03230.28430.3864-0.11520.16320.040.01990.07850.0080.179-20.369-18.2885-10.4002
42.02490.3314-0.31380.4748-0.16912.222-0.0208-0.23730.1040.07010.0280.1343-0.1540.1089-0.0180.22440.0040.01780.0609-0.01020.2039-31.6368-10.8019-6.3324
52.71010.03410.12370.6807-0.00790.8232-0.0092-0.12610.4301-0.0818-0.00810.1392-0.168-0.0670.06120.21130.0056-0.01580.0836-0.0430.2442-36.7726-14.5673-55.0074
63.49721.5369-0.30610.70740.0040.60140.0671-0.79570.94840.2849-0.18060.3763-0.3080.06670.07480.2591-0.0708-0.01840.4864-0.2870.3883-25.2254-6.6372-41.1275
73.4922-0.60351.6934.3691.38484.2695-0.0772-1.1473-0.46140.838-0.153-0.23860.72640.48940.14640.29530.08160.00340.5310.08060.2319-19.3948-19.4364-43.1314
83.49170.1836-0.23661.3025-0.04682.0311-0.1103-0.42890.3554-0.0749-0.07140.15780.05390.19070.02150.17420.0114-0.00490.0547-0.06220.2539-28.4283-14.5831-52.9718
93.21020.0125-0.03490.4231-0.5972.3388-0.0681-1.09940.50520.32430.06880.0125-0.33320.1611-0.00120.22610.04910.0290.7296-0.20140.2791-46.1203-13.8619-38.9706
100.31330.24190.14480.9298-0.44450.4835-0.0491-0.3522-0.214-0.09250.1534-0.16270.1949-0.519-0.12990.2668-0.09370.10590.5523-0.04050.3116-63.9793-25.74264.6
112.48820.15040.9910.803-0.35550.61620.00280.08350.026-0.0643-0.02340.03880.0555-0.01910.02760.1910.01540.03770.33980.00290.2127-66.4198-21.2334-9.3572
121.70420.15511.75820.2317-0.10555.0162-0.16310.8876-0.0257-0.6684-0.2881-0.5638-0.53080.25010.05140.33310.06870.12350.68270.10830.2873-51.4075-20.2078-19.9772
133.4456-0.0731.23290.88610.06691.0390.03550.23010.0052-0.0514-0.13350.03970.0434-0.13550.08640.17680.00610.05090.29320.01280.1957-61.628-21.2944-9.8311
141.9492-0.62021.68710.2817-0.47391.5181-0.1481-0.8155-0.91460.17470.1780.19140.5151-0.23830.04230.38430.07750.20020.3920.15890.4935-68.7325-28.7013-41.8036
153.3899-0.1771-0.06390.70610.81931.1372-0.08980.5337-0.1371-0.02490.02870.0451-0.0296-0.00920.08610.19910.01590.02210.3048-0.01380.2224-76.2176-17.4153-57.651
163.0890.0324-1.28221.9259-0.53232.8238-0.2219-0.835-0.04640.39060.17950.3353-0.2686-0.29830.00990.26550.07690.06710.3861-0.02690.2295-69.2846-17.0077-40.1726
171.0870.0666-0.24091.5835-0.56642.2816-0.24750.2992-0.6919-0.0449-0.08290.09820.59180.10640.05960.23310.02720.07450.1913-0.09540.4027-60.9935-29.4117-57.0448
181.90431.05382.90680.73531.92565.2282-0.03710.61180.208-0.375-0.0485-0.1518-0.73550.56670.06280.2736-0.0270.0140.30410.02770.2227-54.2727-16.9293-62.6766
193.00250.4398-1.06632.25220.6943.512-0.2214-0.42550.08940.13730.2018-0.0516-0.13010.01770.0050.17630.0624-0.02510.163-0.00870.22-59.2462-17.7971-47.1402
203.2715-0.5244-0.69011.6323-0.04682.9643-0.19840.354-0.687-0.013-0.14230.18710.2990.14510.25390.14350.02110.0410.2053-0.0540.3335-65.3483-24.0747-53.4357
212.6826-0.3369-1.69861.6049-1.15742.2788-0.36921.5996-0.9232-0.38580.2897-0.08460.57470.3440.10660.28670.00690.01410.6588-0.20610.3267-80.8434-21.7372-65.0987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 96:109 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 110:180 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 181:229 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 230:288 )A0
5X-RAY DIFFRACTION5CHAIN B AND (RESID 97:163 )B0
6X-RAY DIFFRACTION6CHAIN B AND (RESID 164:180 )B0
7X-RAY DIFFRACTION7CHAIN B AND (RESID 181:194 )B0
8X-RAY DIFFRACTION8CHAIN B AND (RESID 195:274 )B0
9X-RAY DIFFRACTION9CHAIN B AND (RESID 275:288 )B0
10X-RAY DIFFRACTION10CHAIN C AND (RESID 96:109 )C0
11X-RAY DIFFRACTION11CHAIN C AND (RESID 110:176 )C0
12X-RAY DIFFRACTION12CHAIN C AND (RESID 177:194 )C0
13X-RAY DIFFRACTION13CHAIN C AND (RESID 195:289 )C0
14X-RAY DIFFRACTION14CHAIN D AND (RESID 96:112 )D0
15X-RAY DIFFRACTION15CHAIN D AND (RESID 113:140 )D0
16X-RAY DIFFRACTION16CHAIN D AND (RESID 141:155 )D0
17X-RAY DIFFRACTION17CHAIN D AND (RESID 156:176 )D0
18X-RAY DIFFRACTION18CHAIN D AND (RESID 177:194 )D0
19X-RAY DIFFRACTION19CHAIN D AND (RESID 195:229 )D0
20X-RAY DIFFRACTION20CHAIN D AND (RESID 230:274 )D0
21X-RAY DIFFRACTION21CHAIN D AND (RESID 275:288 )D0

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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