[English] 日本語
Yorodumi
- PDB-5w1o: Crystal Structure of HPV16 L1 Pentamer Bound to Heparin Oligosacc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w1o
TitleCrystal Structure of HPV16 L1 Pentamer Bound to Heparin Oligosaccharides
ComponentsMajor capsid protein L1
KeywordsVIRAL PROTEIN / human papillomavirus / jelly roll / capsid protein / receptor HSPG / virus capsid
Function / homology
Function and homology information


T=7 icosahedral viral capsid / symbiont entry into host cell / structural molecule activity / virion attachment to host cell
Similarity search - Function
Major capsid L1 (late) superfamily, Papillomavirus / Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Polyomavirus Vp1; Chain A / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major capsid protein L1
Similarity search - Component
Biological speciesHuman papillomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDasgupta, J. / Chen, X.S.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Structural basis of oligosaccharide receptor recognition by human papillomavirus.
Authors: Dasgupta, J. / Bienkowska-Haba, M. / Ortega, M.E. / Patel, H.D. / Bodevin, S. / Spillmann, D. / Bishop, B. / Sapp, M. / Chen, X.S.
History
DepositionJun 4, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionOct 18, 2017ID: 3OAE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,21716
Polymers237,7485
Non-polymers6,46911
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40000 Å2
ΔGint-179 kcal/mol
Surface area81580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.620, 101.252, 128.182
Angle α, β, γ (deg.)90.00, 90.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Major capsid protein L1 / Late major capsid protein L1


Mass: 47549.547 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus / Gene: L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81007
#2: Polysaccharide
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 500.408 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ad122h-1a_1-5_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-2-deoxy-Glcp6SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1465.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,6,5/[ad122h-1a_1-5_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-2-deoxy-Glcp6SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-2-deoxy-Glcp6SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-2-deoxy-Glcp6SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% PEG400, 0.1 M MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2007
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.797→47.426 Å / Num. obs: 60092 / % possible obs: 98.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.28
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.353

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R5H

2r5h


Resolution: 2.8→47.43 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 29.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 3025 5.04 %
Rwork0.224 --
obs0.226 60060 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16687 0 390 147 17224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01617573
X-RAY DIFFRACTIONf_angle_d1.46923950
X-RAY DIFFRACTIONf_dihedral_angle_d17.6166320
X-RAY DIFFRACTIONf_chiral_restr0.0612634
X-RAY DIFFRACTIONf_plane_restr0.0063069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7971-2.84080.38571160.3142086X-RAY DIFFRACTION79
2.8408-2.88740.38751200.30222419X-RAY DIFFRACTION93
2.8874-2.93720.36841370.292516X-RAY DIFFRACTION96
2.9372-2.99060.36641260.28572609X-RAY DIFFRACTION98
2.9906-3.04810.30971510.27352581X-RAY DIFFRACTION99
3.0481-3.11030.3331370.27312629X-RAY DIFFRACTION99
3.1103-3.17790.30931330.2692619X-RAY DIFFRACTION100
3.1779-3.25180.33331240.26582640X-RAY DIFFRACTION100
3.2518-3.33310.36621620.26492619X-RAY DIFFRACTION100
3.3331-3.42320.31191270.23212606X-RAY DIFFRACTION100
3.4232-3.52390.2781370.22992635X-RAY DIFFRACTION100
3.5239-3.63760.29431440.23492636X-RAY DIFFRACTION100
3.6376-3.76760.26851430.21392631X-RAY DIFFRACTION100
3.7676-3.91840.25921390.21972625X-RAY DIFFRACTION100
3.9184-4.09660.26261440.21072641X-RAY DIFFRACTION100
4.0966-4.31240.21811440.18732628X-RAY DIFFRACTION100
4.3124-4.58240.21761270.18032673X-RAY DIFFRACTION100
4.5824-4.93590.19921210.16582630X-RAY DIFFRACTION100
4.9359-5.4320.21511430.17952654X-RAY DIFFRACTION100
5.432-6.21650.2861430.21832627X-RAY DIFFRACTION99
6.2165-7.82640.24511660.23062642X-RAY DIFFRACTION99
7.8264-47.43270.23871410.22562689X-RAY DIFFRACTION98
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)
12.3936-1.47461.35321.2078-0.69412.5312-0.0479-0.4882-0.72280.03630.28440.46660.3435-0.2431-0.21720.33830.01190.1020.22230.16010.374721.7623-32.833550.7836
21.4195-0.36760.10171.0450.15050.9211-0.1448-0.2933-0.1123-0.01050.24450.37070.2334-0.1598-0.06920.2687-0.04490.0760.2450.15550.376910.048-19.268849.9894
31.3776-0.9838-0.00931.042-0.45391.1014-0.0851-0.2928-0.19370.05560.20950.49050.1631-0.1518-0.08560.1923-0.01780.05260.27990.0710.44228.8827-14.823950.6544
42.3959-0.22661.92481.14970.33332.8691-0.0339-0.4393-0.66730.09920.37650.44940.47-0.2625-0.3380.40350.00560.12780.23550.16150.413218.9284-33.521650.7087
55.89982.1202-2.22815.9042-2.74974.46590.1664-0.14990.07550.0604-0.08460.2030.32130.08220.02280.25780.0657-0.02420.2328-0.03450.107439.9396-31.384746.0088
63.8982-0.35550.63232.0881-1.07571.5001-0.30190.4525-0.1482-0.54170.29650.43680.11510.4268-0.12540.4220.17260.17280.1936-0.2942-0.129938.162-22.296915.2585
71.9165-0.98810.27871.458-0.25730.66820.22610.0689-0.2129-0.4618-0.05940.27410.13580.0886-0.0350.4613-0.0273-0.08030.244-0.04040.16726.7092-20.471717.2817
84.20380.57880.1121.86830.25722.09390.12980.02-0.593-0.43260.14380.64060.5951-0.0674-0.05760.4695-0.0108-0.09610.17950.0070.395316.8025-33.829424.7513
90.6354-0.6105-0.15540.9229-0.10030.9198-0.07210.1639-0.2305-0.04390.06280.47050.2406-0.14290.01510.3257-0.075-0.09950.23860.02970.407311.6108-22.840528.2923
101.8191-3.57110.82928.3617-2.05020.4931-0.4478-0.27750.0920.59280.4409-0.13160.07120.1960.03180.30030.0369-0.01540.4573-0.05550.133541.0332-16.471927.199
111.447-0.27180.01241.01580.17330.26350.07720.25690.0735-0.3918-0.10320.20770.16020.18030.05180.4817-0.0323-0.02650.247-0.02380.181226.3181-13.57728.7706
127.95120.33561.2025.1849-0.16395.09330.19170.9165-0.5458-0.947-0.26290.69380.19450.40350.19160.69190.1835-0.16520.4483-0.2250.125450.2367-41.094320.5361
134.86951.3705-0.36744.94980.56552.17050.09360.4761-0.0976-0.0833-0.024-0.1370.46170.5411-0.05010.47130.11480.0550.3775-0.00470.109345.6033-18.332314.8469
145.10130.2821-0.09512.01210.72851.0546-0.2544-0.00440.4495-0.26410.0511-0.1646-0.15940.28260.17840.3809-0.11350.12440.25010.11640.039539.036516.925111.6044
155.61270.7845-1.11542.7044-0.56770.79390.1770.40650.457-0.187-0.0418-0.0144-0.37940.2963-0.09220.559-0.16210.00370.37940.01540.127536.455320.08846.6764
161.0724-0.17660.01871.7295-0.00011.01150.27480.0289-0.095-0.2195-0.12170.1185-0.04580.1-0.09080.363-0.004-0.02850.20480.08050.203525.31557.882213.5195
175.05261.29990.64852.5428-0.34120.1519-0.13720.5036-0.4182-0.77470.13820.3237-0.01970.3428-0.09130.5601-0.0644-0.11980.41410.06990.175726.2594-2.66810.2535
180.7282-0.1936-0.20531.272-0.06470.9723-0.04840.0564-0.1041-0.42910.09740.33040.1671-0.0402-0.02730.4263-0.0329-0.10660.24030.00550.270419.1433-4.91289.0268
191.5811-0.14740.04950.61230.12360.78050.16360.04470.1203-0.1997-0.06310.0895-0.11890.1418-0.10350.3681-0.0732-0.02630.2840.0540.181127.473815.816616.6563
202.27650.5706-1.2682.76881.97862.7119-0.06671.27620.4443-1.1558-0.3436-0.5962-0.50290.29980.31620.829-0.05860.29270.95550.18880.564258.040810.84340.1964
212.17360.87870.68142.58531.70486.40590.03130.26670.2644-0.18140.2644-0.4701-0.17510.5299-0.14230.4778-0.20130.16770.46790.05640.192944.292321.347716.5976
225.27851.19020.65271.1931-0.34063.2103-0.3634-0.72070.31310.21880.30150.1715-0.93760.1360.04460.3325-0.1133-0.03320.042-0.16090.25424.98732.955444.8472
231.98850.61140.3671.66480.78572.1243-0.0126-0.33120.3640.130.1733-0.1555-0.49390.4797-0.02410.3673-0.11680.02410.3018-0.12620.29923.860933.690644.8604
241.02870.17660.49741.11330.09772.0248-0.04720.06310.0803-0.25760.10030.2893-0.20380.0288-0.07240.2821-0.0011-0.05330.17990.0110.295613.987821.78422.708
257.38683.3869-0.91912.6175-0.6272.28750.18840.0879-0.01760.0074-0.1401-0.0534-0.45330.46130.03740.3381-0.0633-0.07670.2242-0.04650.292326.970127.743241.5658
262.82670.0563-0.29850.65310.39661.6693-0.2436-0.3990.5925-0.12620.27970.1896-0.73280.1972-0.04410.5531-0.07870.00340.187-0.02390.440520.239734.998144.0632
273.16560.34771.36093.38360.16425.5203-0.0078-0.44850.28980.0769-0.05830.0005-0.67570.47650.12840.1828-0.10650.04590.3871-0.10580.347929.428732.099552.161
280.64040.50471.21561.86120.28552.1465-0.32-0.3730.14060.03020.29920.80340.1540.0524-0.02460.14360.2070.27330.5172-0.08780.000512.9693.158770.584
290.05680.39070.22680.95830.47241.7587-0.13330.030.08230.01120.09550.25370.08040.0587-0.00920.16560.04070.10170.27550.06480.27058.46586.290954.573
30-0.0144-0.02820.16980.2676-0.0731.3084-0.0753-0.17940.06230.08960.19640.174-0.1906-0.1632-0.10340.20470.06050.03360.34790.03440.35547.577615.65752.1168
310.6121-0.3198-0.33250.49660.07361.5519-0.1684-0.2052-0.33210.40020.28810.59450.3559-0.62390.09810.2502-0.19280.13620.5890.34620.8147-8.1669-13.800351.4954
322.311.75220.94281.89010.92891.0117-0.1502-0.48140.27690.2268-0.06030.51730.0752-0.16860.23710.26130.12240.11890.5316-0.03940.352514.6437.708573.7231
334.2535-2.6502-2.0156.34561.53258.8644-0.2859-0.317-0.17630.1603-0.0684-0.07080.21220.86630.36230.27560.1943-0.03340.5259-0.0220.170429.1487-6.883171.7811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 20 THROUGH 86 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 87 THROUGH 181 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 182 THROUGH 344 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 345 THROUGH 450 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 451 THROUGH 474 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 20 THROUGH 56 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 57 THROUGH 160 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 161 THROUGH 209 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 210 THROUGH 301 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 302 THROUGH 324 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 325 THROUGH 382 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 383 THROUGH 439 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 440 THROUGH 474 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 20 THROUGH 56 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 57 THROUGH 86 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 87 THROUGH 160 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 161 THROUGH 209 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 210 THROUGH 290 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 291 THROUGH 382 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 383 THROUGH 439 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 440 THROUGH 474 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 20 THROUGH 56 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 57 THROUGH 125 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 126 THROUGH 312 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 313 THROUGH 344 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 345 THROUGH 439 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 440 THROUGH 473 )
28X-RAY DIFFRACTION28CHAIN 'E' AND (RESID 20 THROUGH 86 )
29X-RAY DIFFRACTION29CHAIN 'E' AND (RESID 87 THROUGH 160 )
30X-RAY DIFFRACTION30CHAIN 'E' AND (RESID 161 THROUGH 335 )
31X-RAY DIFFRACTION31CHAIN 'E' AND (RESID 336 THROUGH 356 )
32X-RAY DIFFRACTION32CHAIN 'E' AND (RESID 357 THROUGH 450 )
33X-RAY DIFFRACTION33CHAIN 'E' AND (RESID 451 THROUGH 473 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more