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- PDB-3qw9: Crystal structure of betaglycan ZP-C domain -

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Basic information

Entry
Database: PDB / ID: 3qw9
TitleCrystal structure of betaglycan ZP-C domain
ComponentsTransforming growth factor beta receptor type 3
KeywordsCYTOKINE RECEPTOR / immunoglobulin domain / Zona Pellucida / TGF-beta ligand co-receptor / protein polymerization
Function / homology
Function and homology information


TGF-beta receptor signaling activates SMADs / negative regulation of apoptotic process involved in morphogenesis / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / response to luteinizing hormone / epicardium-derived cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / Signaling by BMP / transforming growth factor beta receptor complex assembly / inhibin-betaglycan-ActRII complex ...TGF-beta receptor signaling activates SMADs / negative regulation of apoptotic process involved in morphogenesis / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / response to luteinizing hormone / epicardium-derived cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / Signaling by BMP / transforming growth factor beta receptor complex assembly / inhibin-betaglycan-ActRII complex / definitive erythrocyte differentiation / muscular septum morphogenesis / response to follicle-stimulating hormone / response to prostaglandin E / BMP binding / vasculogenesis involved in coronary vascular morphogenesis / Signaling by Activin / apoptotic process involved in morphogenesis / secondary palate development / transforming growth factor beta receptor activity / ventricular compact myocardium morphogenesis / collagen metabolic process / negative regulation of epithelial cell migration / regulation of transforming growth factor beta receptor signaling pathway / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor binding / negative regulation of epithelial to mesenchymal transition / type II transforming growth factor beta receptor binding / heart trabecula morphogenesis / activin binding / heart trabecula formation / positive regulation of BMP signaling pathway / glycosaminoglycan binding / transforming growth factor beta binding / definitive hemopoiesis / negative regulation of extracellular matrix assembly / cardiac muscle cell proliferation / ventricular cardiac muscle tissue morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of SMAD protein signal transduction / ventricular septum morphogenesis / roof of mouth development / fibroblast growth factor binding / blood vessel development / outflow tract morphogenesis / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of SMAD protein signal transduction / blastocyst development / epithelial to mesenchymal transition / blood vessel remodeling / vasculogenesis / BMP signaling pathway / animal organ regeneration / coreceptor activity / positive regulation of cardiac muscle cell proliferation / negative regulation of canonical NF-kappaB signal transduction / transforming growth factor beta receptor signaling pathway / liver development / PDZ domain binding / negative regulation of transforming growth factor beta receptor signaling pathway / osteoblast differentiation / negative regulation of epithelial cell proliferation / cell migration / heparin binding / collagen-containing extracellular matrix / protein-containing complex assembly / cell population proliferation / in utero embryonic development / response to hypoxia / receptor complex / intracellular signal transduction / immune response / external side of plasma membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / cell surface / endoplasmic reticulum / signal transduction / extracellular space / membrane / cytoplasm
Similarity search - Function
Zona pellucida, ZP-C domain / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / Immunoglobulin-like ...Zona pellucida, ZP-C domain / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor beta receptor type 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsLin, S.J. / Jardetzky, T.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of betaglycan zona pellucida (ZP)-C domain provides insights into ZP-mediated protein polymerization and TGF-{beta} binding.
Authors: Lin, S.J. / Hu, Y. / Zhu, J. / Woodruff, T.K. / Jardetzky, T.S.
History
DepositionFeb 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transforming growth factor beta receptor type 3
B: Transforming growth factor beta receptor type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2384
Polymers40,1562
Non-polymers2,0822
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-14 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.527, 63.574, 107.217
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transforming growth factor beta receptor type 3 / TGF-beta receptor type 3 / TGFR-3 / Betaglycan / Transforming growth factor beta receptor III / TGF- ...TGF-beta receptor type 3 / TGFR-3 / Betaglycan / Transforming growth factor beta receptor III / TGF-beta receptor type III


Mass: 20078.031 Da / Num. of mol.: 2 / Fragment: unp residues 591-763
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Tgfbr3 / Plasmid: pBACgus-3 / Cell line (production host): High5 / Production host: Trichoplusia Ni (cabbage looper) / References: UniProt: P26342
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3-2/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1203.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-4-2/a3-b1_a4-c1_a6-g1_c4-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 45.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16-18% PEG 6000, 0.1 M Citrate, 0.9-1.0M LiCl2, pH 5.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.11587
SYNCHROTRONSSRL BL11-121.06698
SYNCHROTRONSSRL BL9-231.13993
SYNCHROTRONSSRL BL11-140.91889
Detector
TypeIDDetectorDate
ADSC Q315r1CCDAug 26, 2009
MARCCD 3252CCDApr 9, 2009
MARCCD 3253CCDApr 15, 2009
MARCCD 3254CCDApr 9, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
4SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
21.066981
31.139931
40.918891
ReflectionRedundancy: 6.5 % / Av σ(I) over netI: 31.98 / Number: 207054 / Rmerge(I) obs: 0.148 / Χ2: 2.67 / D res high: 1.84 Å / D res low: 50 Å / Num. obs: 31736 / % possible obs: 98.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.995099.910.0952.68317
3.964.9999.810.1232.82217.9
3.463.9699.510.2132.8718
3.153.4699.710.2682.67410.7
2.923.1598.910.0854.5944
2.752.9299.210.0993.9724
2.612.759910.1183.484.1
2.52.6198.710.1363.1124
2.42.598.510.1642.7224
2.322.499.410.1932.4474
2.252.329810.222.4694
2.182.2597.410.2362.3014
2.122.1898.610.2732.2184
2.072.129810.3151.9824
2.032.0797.110.3772.0044
1.982.0398.910.4321.8814
1.941.989610.5321.7044
1.911.9498.810.7362.1014
1.871.9196.110.9561.6424
1.841.8795.711.6113.8
ReflectionResolution: 1.84→50 Å / Num. obs: 31736 / % possible obs: 98.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.076 / Χ2: 2.669 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.84-1.873.80.38414861.61195.7
1.87-1.9140.95615401.64296.1
1.91-1.9440.73615442.10198.8
1.94-1.9840.53215421.70496
1.98-2.0340.43215811.88198.9
2.03-2.0740.37715462.00497.1
2.07-2.1240.31515461.98298
2.12-2.1840.27316042.21898.6
2.18-2.2540.23615262.30197.4
2.25-2.3240.2215512.46998
2.32-2.440.19315962.44799.4
2.4-2.540.16415872.72298.5
2.5-2.6140.13615723.11298.7
2.61-2.754.10.11816063.4899
2.75-2.9240.09915943.97299.2
2.92-3.1540.08516194.59498.9
3.15-3.4610.70.26816202.67499.7
3.46-3.96180.21316342.8799.5
3.96-4.9917.90.12316702.82299.8
4.99-50170.09517722.68399.9

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Phasing

PhasingMethod: MIRAS
Phasing set
ID
1
2
3
4
Phasing MIRResolution: 1.73→47.71 Å / FOM acentric: 0.171 / FOM centric: 0.245 / Reflection acentric: 31955 / Reflection centric: 3670
Phasing MIR der

Native set-ID: 1 / Resolution: 1.73→47.71 Å

IDDer set-IDPower acentricPower centricReflection acentricReflection centric
ISO_1100319343644
ISO_220.70.642126521060
ISO_330.7430.6755749636
ISO_440.3650.3749523889
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDPower acentricPower centricReflection acentricReflection centric
7.6647.71ISO_100319183
5.457.66ISO_100641200
4.465.45ISO_100855198
3.874.46ISO_1001034203
3.463.87ISO_1001181206
3.163.46ISO_1001308199
2.933.16ISO_1001455210
2.742.93ISO_1001540197
2.582.74ISO_1001651198
2.452.58ISO_1001762198
2.342.45ISO_1001835192
2.242.34ISO_1001925193
2.152.24ISO_1002023193
2.072.15ISO_1002077185
22.07ISO_1002188192
1.942ISO_1002232176
1.881.94ISO_1002259173
1.831.88ISO_1002202143
1.781.83ISO_1001961113
1.731.78ISO_100148692
7.6647.71ISO_21.0560.99731992
5.457.66ISO_21.1060.821641103
4.465.45ISO_20.7530.604855103
3.874.46ISO_20.580.4721034101
3.463.87ISO_20.5480.4921181104
3.163.46ISO_20.5550.451307104
2.933.16ISO_20.5980.4791455106
2.742.93ISO_20.6410.4791540100
2.582.74ISO_20.6460.514165199
2.452.58ISO_20.6520.4651759101
2.342.45ISO_20.6510.48591047
2.242.34ISO_20000
2.152.24ISO_20000
2.072.15ISO_20000
22.07ISO_20000
1.942ISO_20000
1.881.94ISO_20000
1.831.88ISO_20000
1.781.83ISO_20000
1.731.78ISO_20000
7.6647.71ISO_30.9520.9131994
5.457.66ISO_30.980.828641103
4.465.45ISO_30.7560.7855103
3.874.46ISO_30.640.5541034100
3.463.87ISO_30.6430.4291181102
3.163.46ISO_30.6270.4821308103
2.933.16ISO_30.6240.45241131
2.742.93ISO_30000
2.582.74ISO_30000
2.452.58ISO_30000
2.342.45ISO_30000
2.242.34ISO_30000
2.152.24ISO_30000
2.072.15ISO_30000
22.07ISO_30000
1.942ISO_30000
1.881.94ISO_30000
1.831.88ISO_30000
1.781.83ISO_30000
1.731.78ISO_30000
7.6647.71ISO_40.5520.6431993
5.457.66ISO_40.5930.481641103
4.465.45ISO_40.4350.373855103
3.874.46ISO_40.3210.2631034101
3.463.87ISO_40.2710.191181104
3.163.46ISO_40.2340.1751307104
2.933.16ISO_40.2140.1511453106
2.742.93ISO_40.1970.1681536100
2.582.74ISO_40.1870.135119775
2.452.58ISO_40000
2.342.45ISO_40000
2.242.34ISO_40000
2.152.24ISO_40000
2.072.15ISO_40000
22.07ISO_40000
1.942ISO_40000
1.881.94ISO_40000
1.831.88ISO_40000
1.781.83ISO_40000
1.731.78ISO_40000
Phasing MIR shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
7.66-47.710.9090.773320193
5.45-7.660.8480.697641200
4.46-5.450.7740.616855198
3.87-4.460.6870.5221034203
3.46-3.870.6030.4651181206
3.16-3.460.530.4451308199
2.93-3.160.3910.2861455210
2.74-2.930.3090.2681541199
2.58-2.740.2270.2211655203
2.45-2.580.1740.1471773202
2.34-2.450.0710.0541839197
2.24-2.34001925193
2.15-2.24002023193
2.07-2.15002077185
2-2.07002188192
1.94-2002232176
1.88-1.94002259173
1.83-1.88002202143
1.78-1.83001961113
1.73-1.7800148692

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MIRAS / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2833 / WRfactor Rwork: 0.2142 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8247 / SU B: 9.632 / SU ML: 0.128 / SU R Cruickshank DPI: 0.1908 / SU Rfree: 0.1776 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 1278 5.1 %RANDOM
Rwork0.1859 ---
obs0.189 25073 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.33 Å2 / Biso mean: 39.447 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--0.4 Å2-0 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 140 173 2977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222901
X-RAY DIFFRACTIONr_bond_other_d0.0010.021942
X-RAY DIFFRACTIONr_angle_refined_deg1.9822.023961
X-RAY DIFFRACTIONr_angle_other_deg1.29734743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5195336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83724.261115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36915467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0481510
X-RAY DIFFRACTIONr_chiral_restr0.2030.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213012
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
X-RAY DIFFRACTIONr_mcbond_it6.06321701
X-RAY DIFFRACTIONr_mcbond_other2.2052660
X-RAY DIFFRACTIONr_mcangle_it7.90132784
X-RAY DIFFRACTIONr_scbond_it8.31521200
X-RAY DIFFRACTIONr_scangle_it10.84931176
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 76 -
Rwork0.228 1727 -
all-1803 -
obs--97.35 %
Refinement TLS params.Method: refined / Origin x: 0.0935 Å / Origin y: 34.9376 Å / Origin z: 11.1624 Å
111213212223313233
T0.0723 Å2-0.0205 Å20.0109 Å2-0.0201 Å20.0188 Å2--0.0681 Å2
L3.0578 °2-0.8277 °2-0.1633 °2-0.7111 °2-0.2126 °2--0.9009 °2
S0.0444 Å °0.0406 Å °0.0018 Å °-0.0362 Å °-0.009 Å °-0.088 Å °0.0999 Å °-0.0181 Å °-0.0354 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 179
2X-RAY DIFFRACTION1B12 - 178

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Yorodumi

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  • 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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