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- PDB-3zpv: Crystal structure of Drosophila Pygo PHD finger in complex with L... -

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Basic information

Entry
Database: PDB / ID: 3zpv
TitleCrystal structure of Drosophila Pygo PHD finger in complex with Legless HD1 domain
Components
  • (PROTEIN PYGOPUS) x 2
  • PROTEIN BCL9 HOMOLOG
KeywordsTRANSCRIPTION / WNT SIGNALING PATHWAY / ZN FINGER / HISTONE H3 TAIL BINDING
Function / homology
Function and homology information


sternite morphogenesis / leg disc pattern formation / chitin-based larval cuticle pattern formation / imaginal disc-derived wing expansion / delamination / Formation of the beta-catenin:TCF transactivating complex / Transport of ARM to the nucleus / Transcription activation by ARM / eye-antennal disc development / imaginal disc-derived wing margin morphogenesis ...sternite morphogenesis / leg disc pattern formation / chitin-based larval cuticle pattern formation / imaginal disc-derived wing expansion / delamination / Formation of the beta-catenin:TCF transactivating complex / Transport of ARM to the nucleus / Transcription activation by ARM / eye-antennal disc development / imaginal disc-derived wing margin morphogenesis / wing disc morphogenesis / segment polarity determination / beta-catenin-TCF complex / embryonic pattern specification / canonical Wnt signaling pathway / methylated histone binding / transcription coactivator activity / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
B-cell lymphoma 9, beta-catenin binding domain / B-cell lymphoma 9 protein / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger ...B-cell lymphoma 9, beta-catenin binding domain / B-cell lymphoma 9 protein / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein BCL9 homolog / Protein pygopus
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsMiller, T.C.R. / Mieszczanek, J. / Sanchez-Barrena, M.J. / Rutherford, T.J. / Fiedler, M. / Bienz, M.
CitationJournal: Structure / Year: 2013
Title: Evolutionary Adaptation of the Fly Pygo Phd Finger Towards Recognizing Histone H3 Tail Methylated at Arginine 2
Authors: Miller, T.C.R. / Mieszczanek, J. / Sanchez-Barrena, M.J. / Rutherford, T.J. / Fiedler, M. / Bienz, M.
History
DepositionMar 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Database references
Revision 1.3Feb 19, 2014Group: Atomic model / Database references ...Atomic model / Database references / Source and taxonomy / Structure summary
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
0: PROTEIN BCL9 HOMOLOG
1: PROTEIN PYGOPUS
2: PROTEIN BCL9 HOMOLOG
3: PROTEIN PYGOPUS
4: PROTEIN BCL9 HOMOLOG
5: PROTEIN PYGOPUS
6: PROTEIN BCL9 HOMOLOG
7: PROTEIN PYGOPUS
8: PROTEIN BCL9 HOMOLOG
9: PROTEIN PYGOPUS
A: PROTEIN PYGOPUS
B: PROTEIN BCL9 HOMOLOG
C: PROTEIN PYGOPUS
D: PROTEIN BCL9 HOMOLOG
E: PROTEIN PYGOPUS
F: PROTEIN BCL9 HOMOLOG
G: PROTEIN PYGOPUS
H: PROTEIN BCL9 HOMOLOG
I: PROTEIN PYGOPUS
J: PROTEIN BCL9 HOMOLOG
K: PROTEIN PYGOPUS
L: PROTEIN BCL9 HOMOLOG
M: PROTEIN PYGOPUS
N: PROTEIN BCL9 HOMOLOG
O: PROTEIN PYGOPUS
P: PROTEIN BCL9 HOMOLOG
Q: PROTEIN PYGOPUS
R: PROTEIN BCL9 HOMOLOG
S: PROTEIN PYGOPUS
T: PROTEIN BCL9 HOMOLOG
U: PROTEIN PYGOPUS
V: PROTEIN BCL9 HOMOLOG
W: PROTEIN PYGOPUS
X: PROTEIN BCL9 HOMOLOG
Y: PROTEIN PYGOPUS
Z: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,41572
Polymers197,06036
Non-polymers2,35536
Water6,684371
1
A: PROTEIN PYGOPUS
B: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-11.8 kcal/mol
Surface area6640 Å2
MethodPISA
2
C: PROTEIN PYGOPUS
D: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-11.7 kcal/mol
Surface area6610 Å2
MethodPISA
3
E: PROTEIN PYGOPUS
F: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0904
Polymers10,9592
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-12.3 kcal/mol
Surface area6570 Å2
MethodPISA
4
G: PROTEIN PYGOPUS
H: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-12.8 kcal/mol
Surface area6640 Å2
MethodPISA
5
I: PROTEIN PYGOPUS
J: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-12.7 kcal/mol
Surface area6530 Å2
MethodPISA
6
K: PROTEIN PYGOPUS
L: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-12.6 kcal/mol
Surface area6570 Å2
MethodPISA
7
M: PROTEIN PYGOPUS
N: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-11.6 kcal/mol
Surface area6500 Å2
MethodPISA
8
O: PROTEIN PYGOPUS
P: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0904
Polymers10,9592
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-12 kcal/mol
Surface area6590 Å2
MethodPISA
9
Q: PROTEIN PYGOPUS
R: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-11.9 kcal/mol
Surface area6580 Å2
MethodPISA
10
S: PROTEIN PYGOPUS
T: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-12.2 kcal/mol
Surface area6520 Å2
MethodPISA
11
U: PROTEIN PYGOPUS
V: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-12.2 kcal/mol
Surface area6500 Å2
MethodPISA
12
W: PROTEIN PYGOPUS
X: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-11.8 kcal/mol
Surface area6580 Å2
MethodPISA
13
Y: PROTEIN PYGOPUS
Z: PROTEIN BCL9 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0904
Polymers10,9592
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-12.2 kcal/mol
Surface area6630 Å2
MethodPISA
14
0: PROTEIN BCL9 HOMOLOG
1: PROTEIN PYGOPUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-12 kcal/mol
Surface area6540 Å2
MethodPISA
15
2: PROTEIN BCL9 HOMOLOG
3: PROTEIN PYGOPUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-11.9 kcal/mol
Surface area6590 Å2
MethodPISA
16
4: PROTEIN BCL9 HOMOLOG
5: PROTEIN PYGOPUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-12.3 kcal/mol
Surface area6510 Å2
MethodPISA
17
6: PROTEIN BCL9 HOMOLOG
7: PROTEIN PYGOPUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-12.3 kcal/mol
Surface area6590 Å2
MethodPISA
18
8: PROTEIN BCL9 HOMOLOG
9: PROTEIN PYGOPUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0764
Polymers10,9452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-11.8 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.210, 111.960, 190.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
PROTEIN BCL9 HOMOLOG / PROTEIN LEGLESS / PROTEIN LEGLESS


Mass: 3987.497 Da / Num. of mol.: 18 / Fragment: HD1 DOMAIN, RESIDUES 321-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: BI-CISTRONIC EXPRESSION VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: Q961D9
#2: Protein
PROTEIN PYGOPUS / PROTEIN GAMMY LEGS / PROTEIN GAMMY LEGS


Mass: 6957.963 Da / Num. of mol.: 15 / Fragment: PHD DOMAIN, RESIDUES 747-804
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: BI-CISTRONIC EXPRESSION VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: Q9V9W8
#3: Protein PROTEIN PYGOPUS / PROTEIN GAMMY LEGS / PROTEIN GAMMY LEGS


Mass: 6971.989 Da / Num. of mol.: 3 / Fragment: PHD DOMAIN, RESIDUES 747-804
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: BI-CISTRONIC EXPRESSION VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: Q9V9W8
#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.31 Å3/Da / Density % sol: 46.83 % / Description: NONE
Crystal growDetails: 1.136 M (NH4)2SO4, 100 MM TRIS PH 8.3, 200 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.2843
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 14, 2007
RadiationMonochromator: SINGLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2843 Å / Relative weight: 1
ReflectionResolution: 2.68→46.18 Å / Num. obs: 63722 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.7
Reflection shellResolution: 2.68→2.82 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0024refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VP7

2vp7


Resolution: 2.68→46.24 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.551 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 1.119 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26231 3222 5.1 %RANDOM
Rwork0.22389 ---
obs0.22582 60454 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.824 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---1.54 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.68→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13607 0 36 371 14014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913953
X-RAY DIFFRACTIONr_bond_other_d0.0090.0212514
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.89918801
X-RAY DIFFRACTIONr_angle_other_deg1.859328773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11251753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91525.304690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.418152210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9221518
X-RAY DIFFRACTIONr_chiral_restr0.0940.22025
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216305
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023549
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 226 -
Rwork0.332 4454 -
obs--99.98 %

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