[English] 日本語
Yorodumi
- PDB-5w1x: Crystal Structure of Humanpapillomavirus18 (HPV18) Capsid L1 Pent... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w1x
TitleCrystal Structure of Humanpapillomavirus18 (HPV18) Capsid L1 Pentamers Bound to Heparin Oligosaccharides
ComponentsMajor capsid protein L1
KeywordsVIRAL PROTEIN / protein oligosaccharide complex / jelly roll / capsid protein / binds to host receptor / receptor heparin oligosaccharides / virus capsid
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / membrane
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 / Major capsid protein L1
Similarity search - Component
Biological speciesHuman papillomavirus type 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.374 Å
AuthorsChen, X.S. / Dasgupta, J.
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 5, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionDec 12, 2018ID: 3OFL
Revision 1.0Dec 12, 2018Provider: 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 / _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_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_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_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
F: Major capsid protein L1
G: Major capsid protein L1
H: Major capsid protein L1
I: Major capsid protein L1
J: Major capsid protein L1
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
O: Major capsid protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)734,41945
Polymers712,17015
Non-polymers22,24830
Water00
1
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)247,79120
Polymers237,3905
Non-polymers10,40015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44290 Å2
ΔGint-143 kcal/mol
Surface area81650 Å2
MethodPISA
2
F: Major capsid protein L1
G: Major capsid protein L1
H: Major capsid protein L1
I: Major capsid protein L1
J: Major capsid protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,25313
Polymers237,3905
Non-polymers7,8628
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43200 Å2
ΔGint-159 kcal/mol
Surface area79600 Å2
MethodPISA
3
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
O: Major capsid protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,37512
Polymers237,3905
Non-polymers3,9857
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39570 Å2
ΔGint-162 kcal/mol
Surface area78340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.993, 106.490, 237.661
Angle α, β, γ (deg.)88.46, 85.75, 69.02
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Major capsid protein L1


Mass: 47478.031 Da / Num. of mol.: 15 / Mutation: N98D,C226S,H444Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 18 / Gene: L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5G244, UniProt: P06794*PLUS
#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.: 19
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


Type: oligosaccharide / Mass: 982.800 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[ad122h-1a_1-5_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][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: 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
#5: 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-(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: 2429.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,10,9/[ad122h-1a_1-5_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1_h4-i1_i4-j1WURCSPDB2Glycan 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-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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 20% PEG3350, 0.2 M potassium acetate, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 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: 3.374→42.794 Å / Num. obs: 92923 / % possible obs: 90 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.27
Reflection shellResolution: 3.374→3.829 Å / Rmerge(I) obs: 0.274

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R5I

2r5i


Resolution: 3.374→42.794 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.17
RfactorNum. reflection% reflection
Rfree0.2339 4607 4.96 %
Rwork0.1709 --
obs0.174 92872 89.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.374→42.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49725 0 1350 0 51075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00452830
X-RAY DIFFRACTIONf_angle_d0.91172044
X-RAY DIFFRACTIONf_dihedral_angle_d15.35418982
X-RAY DIFFRACTIONf_chiral_restr0.0387897
X-RAY DIFFRACTIONf_plane_restr0.0049151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3739-3.41220.4202400.2491805X-RAY DIFFRACTION55
3.4122-3.45230.31721060.21882440X-RAY DIFFRACTION73
3.4523-3.49440.35731360.22762525X-RAY DIFFRACTION76
3.4944-3.53860.33691440.23922613X-RAY DIFFRACTION79
3.5386-3.58520.31911340.26532620X-RAY DIFFRACTION81
3.5852-3.63430.33941360.24742696X-RAY DIFFRACTION82
3.6343-3.68620.41421590.28972765X-RAY DIFFRACTION83
3.6862-3.74110.32141380.23312737X-RAY DIFFRACTION84
3.7411-3.79960.33631470.21792804X-RAY DIFFRACTION85
3.7996-3.86180.22851520.18572904X-RAY DIFFRACTION87
3.8618-3.92840.26541700.19152816X-RAY DIFFRACTION88
3.9284-3.99980.2731430.21662911X-RAY DIFFRACTION87
3.9998-4.07660.24211710.1772980X-RAY DIFFRACTION90
4.0766-4.15980.24441600.16382881X-RAY DIFFRACTION89
4.1598-4.25010.1911500.14783054X-RAY DIFFRACTION91
4.2501-4.34890.19481460.14632914X-RAY DIFFRACTION90
4.3489-4.45760.20991870.14733063X-RAY DIFFRACTION92
4.4576-4.5780.21971620.14082985X-RAY DIFFRACTION92
4.578-4.71250.17761730.13273087X-RAY DIFFRACTION93
4.7125-4.86440.19011720.11993102X-RAY DIFFRACTION94
4.8644-5.0380.18731860.12983177X-RAY DIFFRACTION97
5.038-5.23940.18161620.13493182X-RAY DIFFRACTION98
5.2394-5.47740.20051660.1383277X-RAY DIFFRACTION99
5.4774-5.76550.2091570.15153309X-RAY DIFFRACTION99
5.7655-6.12580.21961700.16033227X-RAY DIFFRACTION99
6.1258-6.59720.21511690.16293281X-RAY DIFFRACTION99
6.5972-7.25820.2371770.15933260X-RAY DIFFRACTION99
7.2582-8.30180.19921610.15943312X-RAY DIFFRACTION100
8.3018-10.43430.16831750.13093264X-RAY DIFFRACTION100
10.4343-42.79750.23811580.19523274X-RAY DIFFRACTION99
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)
13.6522.1334-0.47792.9844-0.35012.49720.2011-0.01820.20990.0362-0.04410.2607-0.3224-0.1754-0.15530.45110.1987-0.06170.34450.08480.3971-9.932325.73-9.1665
21.55090.71330.57893.87851.20181.4612-0.11020.38160.0549-0.7230.07250.2275-0.2596-0.12780.00690.50940.0729-0.02760.55640.06020.453-13.54411.2724-23.6688
33.32422.943-0.15933.6072-0.68021.58640.1401-0.0140.4788-0.1059-0.00480.2005-0.4326-0.0383-0.11020.64430.1460.08470.3684-0.01710.4814-5.93131.5156-5.6818
42.57961.50521.06373.45660.66272.6506-0.0204-0.1890.12350.0838-0.13110.3696-0.2649-0.41780.15120.38580.14760.11910.3294-0.07950.4274-11.405316.377421.6233
51.88381.01030.9381.51530.6311.7268-0.0603-0.05970.3630.0057-0.08920.2766-0.4033-0.21270.15110.45010.12970.06140.386-0.05680.4292-11.393816.055818.383
63.87840.55541.5241.64110.57642.07550.0554-0.21730.04370.0776-0.06890.119-0.0927-0.3161-0.01180.3469-0.00030.03980.26120.09030.27123.4529-15.094725.5488
72.6874-0.34220.77080.7851-0.2841.6717-0.1159-0.16070.07840.17020.03680.0160.1227-0.23630.08590.4307-0.01260.03980.25710.03820.32791.7637-12.416824.3606
85.60290.34280.47561.6497-0.40772.2308-0.01490.1436-0.3264-0.1925-0.0140.18630.1963-0.08850.0190.39540.0654-0.04270.1498-0.0570.315814.8617-23.7419-8.0761
93.47830.1816-0.4530.4508-0.24861.3143-0.0033-0.0361-0.5219-0.1409-0.01990.07990.3195-0.0190.02960.48640.0146-0.00670.2491-0.05850.444912.0503-25.0187-2.4641
104.56320.9515-0.56522.141-0.2411.4733-0.09130.28990.0164-0.25840.06240.19730.125-0.26540.03920.42190.0583-0.04220.4548-0.06530.16635.6884-0.88-29.1984
111.2951-0.20920.00881.3433-0.53792.3758-0.07360.1591-0.1897-0.13690.01760.06360.2971-0.27890.03340.35440.0358-0.03460.4338-0.05280.38620.1862-14.7939-21.3421
125.45730.6268-1.3320.91310.07470.75620.15610.64980.3986-0.1802-0.1456-0.0207-0.1423-0.1989-0.03330.51320.0825-0.03590.36980.10490.2910.46078.225-31.3321
133.76551.61552.04333.20691.79323.5161-0.0023-0.42310.03530.0896-0.15260.2428-0.0549-0.29830.13010.44410.00510.16440.40280.01040.326238.639350.9177100.3309
142.16010.54491.10920.62030.53172.01-0.0915-0.24390.18450.0883-0.05820.1477-0.3192-0.04570.16840.504-0.03410.09950.4693-0.02260.403235.920854.815196.0526
152.9693-1.23680.96550.59070.03531.9906-0.16240.3886-0.06460.15970.4631-0.20550.06660.7449-0.36110.4564-0.0363-0.03050.72490.03750.376363.08520.807795.0925
165.6314-0.54892.91563.38450.09964.49090.023-0.2302-0.8595-0.18790.1637-0.4230.7530.7584-0.24460.37710.06930.11390.65770.13790.523559.672614.18394.3415
170.51440.96-0.58913.17140.79833.1846-0.1657-0.1893-0.20240.44860.4214-0.39650.0231.0482-0.32250.49920.2101-0.04840.61810.01270.307962.090222.553593.9697
183.487-0.09611.81761.83610.5451.8998-0.298-0.69380.19470.13330.1260.556-0.4071-0.52210.09380.6211-0.06360.14510.66060.04950.541633.048127.476691.4407
191.6056-0.6904-0.10381.0094-0.00491.5632-0.041-0.3288-0.04360.04590.06730.12820.1609-0.1542-0.01280.4397-0.08510.01880.3470.05980.476544.398926.321490.3037
202.1284-0.6541.31231.63181.27123.79560.0546-0.88110.05070.6510.1808-0.13380.79270.914-0.1240.76130.0687-0.03770.88180.00960.630170.044620.9423102.5517
214.96490.44550.82041.0351-0.28941.84730.04550.1663-0.2427-0.076-0.04060.09990.16580.01190.03550.42520.04110.04550.0983-0.0470.375763.426823.609958.6886
223.31220.2084-0.20890.3493-0.01690.79570.079-0.223-0.4593-0.0543-0.08340.02750.21750.05810.03470.49470.0071-0.00270.2518-0.01430.479660.613520.781763.6758
234.97870.9603-0.26472.07040.01971.5779-0.04780.22790.1353-0.2460.007-0.1277-0.0705-0.14830.05130.40830.0283-0.01070.1920.05780.261854.072654.573846.9099
242.56011.4557-0.29211.5519-0.19880.7045-0.12130.2101-0.1759-0.22960.0451-0.34170.0098-0.09970.07070.48350.0624-0.01430.28830.03030.374254.43348.207646.6416
254.76142.65490.03143.7274-0.56542.01310.1252-0.44610.1592-0.0145-0.11390.1596-0.4211-0.15790.02540.53660.08020.06470.23840.01610.31738.659971.436572.4524
262.30611.44950.16442.43950.35860.91870.037-0.00340.3514-0.10570.09430.2116-0.468-0.0072-0.11240.55220.06170.04470.27830.00120.452839.042969.223466.4993
273.64550.92492.11032.45781.11723.46940.0852-0.2255-0.13660.1845-0.06150.2270.2029-0.421-0.05130.39610.02690.19160.4929-0.00010.355985.006157.4617186.6297
282.4847-0.50651.61861.9905-0.37433.4492-0.2057-0.34910.17110.06740.140.3265-0.4087-0.51670.00250.49520.03690.07370.4559-0.02610.492774.216269.4892176.4538
292.06641.30262.14272.21132.48623.25030.1538-0.2503-0.15870.4501-0.1329-0.01190.4611-0.2121-0.04570.55020.0330.07170.3660.13040.368690.59655.413192.6723
303.8955-0.36761.74511.622-0.41653.14320.03890.1826-0.2556-0.1022-0.05050.01490.2705-0.00960.03390.4107-0.03760.06590.32580.0070.3748100.409233.6877166.8905
313.2304-1.1920.49171.3956-0.34321.1949-0.1133-0.1458-0.3870.05750.0860.22920.178-0.20490.0070.4469-0.05760.02160.4162-0.02550.438595.657336.0124170.8866
324.22310.08020.71251.7252-0.36291.1746-0.01690.3447-0.1168-0.2002-0.01970.05370.0254-0.02610.03850.54820.04210.03410.6345-0.13390.3031109.763549.0538137.701
332.55760.272-0.15431.0994-0.02190.8582-0.04130.2128-0.3453-0.2347-0.02440.07650.0353-0.01320.07150.4520.002-0.01430.6772-0.10660.3587106.981444.4225141.2313
344.47681.3650.05742.62590.52761.3860.07360.15350.3223-0.03130.12280.153-0.1533-0.1129-0.16030.45290.06690.03430.60760.07880.2355100.149481.9313139.449
351.39320.77850.07511.58470.06141.1498-0.02490.4101-0.0226-0.29140.139-0.02960.0042-0.0746-0.11060.470.0632-0.01720.7383-0.00610.3956100.5976.211136.6422
365.05032.46661.58333.49111.05372.37780.01070.10490.2468-0.04150.04530.3513-0.2082-0.0791-0.04340.40360.14940.0820.32570.08370.306284.906387.1417169.5519
371.51760.72590.53781.89271.59022.5736-0.18750.3150.2765-0.52140.0240.3021-0.513-0.34720.17120.55360.0671-0.01180.71250.10330.484482.029584.4885150.799
383.74991.88181.1722.90370.4961.29020.0790.0680.2070.1638-0.0090.2472-0.3194-0.1263-0.07250.58250.10690.15090.5031-0.05040.289388.645290.5646176.3159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 160 )
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 298 )
3X-RAY DIFFRACTION3chain 'A' and (resid 299 through 474 )
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 181 )
5X-RAY DIFFRACTION5chain 'B' and (resid 182 through 474 )
6X-RAY DIFFRACTION6chain 'C' and (resid 20 through 181 )
7X-RAY DIFFRACTION7chain 'C' and (resid 182 through 474 )
8X-RAY DIFFRACTION8chain 'D' and (resid 20 through 160 )
9X-RAY DIFFRACTION9chain 'D' and (resid 161 through 474 )
10X-RAY DIFFRACTION10chain 'E' and (resid 20 through 181 )
11X-RAY DIFFRACTION11chain 'E' and (resid 182 through 309 )
12X-RAY DIFFRACTION12chain 'E' and (resid 310 through 474 )
13X-RAY DIFFRACTION13chain 'F' and (resid 20 through 160 )
14X-RAY DIFFRACTION14chain 'F' and (resid 161 through 474 )
15X-RAY DIFFRACTION15chain 'G' and (resid 20 through 56 )
16X-RAY DIFFRACTION16chain 'G' and (resid 57 through 86 )
17X-RAY DIFFRACTION17chain 'G' and (resid 87 through 125 )
18X-RAY DIFFRACTION18chain 'G' and (resid 126 through 181 )
19X-RAY DIFFRACTION19chain 'G' and (resid 182 through 383 )
20X-RAY DIFFRACTION20chain 'G' and (resid 384 through 474 )
21X-RAY DIFFRACTION21chain 'H' and (resid 20 through 160 )
22X-RAY DIFFRACTION22chain 'H' and (resid 161 through 474 )
23X-RAY DIFFRACTION23chain 'I' and (resid 20 through 160 )
24X-RAY DIFFRACTION24chain 'I' and (resid 161 through 474 )
25X-RAY DIFFRACTION25chain 'J' and (resid 20 through 160 )
26X-RAY DIFFRACTION26chain 'J' and (resid 161 through 474 )
27X-RAY DIFFRACTION27chain 'K' and (resid 20 through 160 )
28X-RAY DIFFRACTION28chain 'K' and (resid 161 through 309 )
29X-RAY DIFFRACTION29chain 'K' and (resid 310 through 474 )
30X-RAY DIFFRACTION30chain 'L' and (resid 20 through 160 )
31X-RAY DIFFRACTION31chain 'L' and (resid 161 through 474 )
32X-RAY DIFFRACTION32chain 'M' and (resid 20 through 160 )
33X-RAY DIFFRACTION33chain 'M' and (resid 161 through 474 )
34X-RAY DIFFRACTION34chain 'N' and (resid 20 through 160 )
35X-RAY DIFFRACTION35chain 'N' and (resid 161 through 474 )
36X-RAY DIFFRACTION36chain 'O' and (resid 20 through 160 )
37X-RAY DIFFRACTION37chain 'O' and (resid 161 through 309 )
38X-RAY DIFFRACTION38chain 'O' and (resid 310 through 474 )

+
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