[English] 日本語
Yorodumi
- PDB-5e65: The complex structure of Hemagglutinin-esterase-fusion mutant pro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5.0E+65
TitleThe complex structure of Hemagglutinin-esterase-fusion mutant protein from the influenza D virus with receptor analog 9-O-Ac-3'SLN (Tr322)
Components(Hemagglutinin- ...) x 2
KeywordsHYDROLASE / influenza virus / HEF / membrane
Function / homology
Function and homology information


sialate O-acetylesterase activity / sialate O-acetylesterase / host cell surface receptor binding / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / plasma membrane
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #20 / Haemagglutinin stalk, influenza C / Influenza C hemagglutinin stalk / Haemagglutinin-esterase glycoprotein, haemagglutinin domain / Haemagglutinin-esterase glycoprotein, core / Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein / Hemagglutinin esterase / Ubiquitin Ligase Nedd4; Chain: W; / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B ...Ubiquitin Ligase Nedd4; Chain: W; - #20 / Haemagglutinin stalk, influenza C / Influenza C hemagglutinin stalk / Haemagglutinin-esterase glycoprotein, haemagglutinin domain / Haemagglutinin-esterase glycoprotein, core / Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein / Hemagglutinin esterase / Ubiquitin Ligase Nedd4; Chain: W; / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Single Sheet / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin-esterase-fusion glycoprotein
Similarity search - Component
Biological speciesInfluenza D virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSong, H. / Qi, J. / Shi, Y. / Gao, G.F.
CitationJournal: PLoS Pathog. / Year: 2016
Title: An Open Receptor-Binding Cavity of Hemagglutinin-Esterase-Fusion Glycoprotein from Newly-Identified Influenza D Virus: Basis for Its Broad Cell Tropism
Authors: Song, H. / Qi, J. / Khedri, Z. / Diaz, S. / Yu, H. / Chen, X. / Varki, A. / Shi, Y. / Gao, G.F.
History
DepositionOct 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _pdbx_struct_oper_list.symmetry_operation
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_validate_close_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_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.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 2.1Nov 8, 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin-esterase
B: Hemagglutinin-esterase
C: Hemagglutinin-esterase
D: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,74716
Polymers127,9374
Non-polymers6,81012
Water12,160675
1
A: Hemagglutinin-esterase
B: Hemagglutinin-esterase
hetero molecules

A: Hemagglutinin-esterase
B: Hemagglutinin-esterase
hetero molecules

A: Hemagglutinin-esterase
B: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,09424
Polymers191,9066
Non-polymers11,18818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area46360 Å2
ΔGint90 kcal/mol
Surface area67070 Å2
MethodPISA
2
C: Hemagglutinin-esterase
D: Hemagglutinin-esterase
hetero molecules

C: Hemagglutinin-esterase
D: Hemagglutinin-esterase
hetero molecules

C: Hemagglutinin-esterase
D: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,14824
Polymers191,9066
Non-polymers9,24218
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area42930 Å2
ΔGint46 kcal/mol
Surface area66880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.897, 164.897, 164.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

-
Components

-
Hemagglutinin- ... , 2 types, 4 molecules ACBD

#1: Protein Hemagglutinin-esterase


Mass: 46456.988 Da / Num. of mol.: 2 / Fragment: UNP residues 19-445 / Mutation: S57A, D356A, H359A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza D virus (D/swine/Oklahoma/1334/2011)
Strain: D/swine/Oklahoma/1334/2011 / Gene: HEF / Plasmid: PFASTBAC1 / Cell line (production host): HI5 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: K9LG83
#2: Protein Hemagglutinin-esterase


Mass: 17511.521 Da / Num. of mol.: 2 / Fragment: UNP residues 456-621
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza D virus (D/swine/Oklahoma/1334/2011)
Strain: D/swine/Oklahoma/1334/2011 / Gene: HEF / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: K9LG83

-
Sugars , 4 types, 12 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-3)-beta-D- ...9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 513.448 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O_9*OCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac9Ac]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 1 types, 675 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M PCTP (Propionic acid, Cacodylate, Bis-tris propane system) buffer pH 8.5, 22.5 % w/v PEG 1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.199→50 Å / Num. obs: 75424 / % possible obs: 99.6 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 24.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.596 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E5W

5e5w


Resolution: 2.2→47.602 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 3800 5.04 %
Rwork0.2035 --
obs0.2055 75424 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→47.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8700 0 454 675 9829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069388
X-RAY DIFFRACTIONf_angle_d1.00512736
X-RAY DIFFRACTIONf_dihedral_angle_d13.2263432
X-RAY DIFFRACTIONf_chiral_restr0.0421442
X-RAY DIFFRACTIONf_plane_restr0.0041608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1992-2.22710.29341340.25762480X-RAY DIFFRACTION94
2.2271-2.25640.32261060.25862602X-RAY DIFFRACTION98
2.2564-2.28730.30241520.24672623X-RAY DIFFRACTION99
2.2873-2.31990.29551470.2382616X-RAY DIFFRACTION100
2.3199-2.35460.26841420.22992661X-RAY DIFFRACTION100
2.3546-2.39140.28811420.24042621X-RAY DIFFRACTION100
2.3914-2.43060.29681520.22442619X-RAY DIFFRACTION100
2.4306-2.47250.23931310.22382659X-RAY DIFFRACTION100
2.4725-2.51740.25421460.22962601X-RAY DIFFRACTION100
2.5174-2.56580.29871320.22422680X-RAY DIFFRACTION100
2.5658-2.61820.27571510.22552640X-RAY DIFFRACTION100
2.6182-2.67510.23971330.21792654X-RAY DIFFRACTION100
2.6751-2.73740.26941350.22062643X-RAY DIFFRACTION100
2.7374-2.80580.28331310.22242661X-RAY DIFFRACTION100
2.8058-2.88170.27541480.21412657X-RAY DIFFRACTION100
2.8817-2.96640.25461250.21412657X-RAY DIFFRACTION100
2.9664-3.06220.27331310.22362671X-RAY DIFFRACTION100
3.0622-3.17160.22521310.22132660X-RAY DIFFRACTION100
3.1716-3.29860.24241520.21442663X-RAY DIFFRACTION100
3.2986-3.44860.24491220.20042659X-RAY DIFFRACTION100
3.4486-3.63040.22411250.1892698X-RAY DIFFRACTION100
3.6304-3.85780.2231490.1832661X-RAY DIFFRACTION100
3.8578-4.15550.23351660.16972658X-RAY DIFFRACTION100
4.1555-4.57330.19461620.16542692X-RAY DIFFRACTION100
4.5733-5.23440.20181450.16332684X-RAY DIFFRACTION100
5.2344-6.5920.24351650.19792725X-RAY DIFFRACTION100
6.592-47.61280.23391450.21472779X-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)
10.29760.0464-0.44990.0409-0.1260.6517-0.2897-0.10980.747-0.26910.0742-0.0916-0.862-0.34330.09320.5994-0.0504-0.09440.3161-0.02960.637711.976727.0273-0.0881
20.07540.00340.1180.05420.0670.106-0.0885-0.0246-0.0029-0.1133-0.1089-0.2551-0.04160.1973-00.3752-0.0472-0.01120.32440.01160.37523.380614.4053-7.7811
30.14010.3995-0.28550.31680.56330.12120.0003-0.0102-0.09580.0472-0.0335-0.12130.04070.0633-00.32610.08810.0280.23190.01730.2521.274-12.819-32.161
40.3459-0.05990.30690.8102-0.3392-0.20210.0510.1447-0.0964-0.07970.0503-0.0202-0.02380.02970.00080.30580.08220.03240.27690.02140.2157-3.7909-27.3004-50.4747
50.26230.3119-0.11840.371-0.21990.11920.0549-0.0172-0.12080.06860.03370.3313-0.0885-0.091900.28930.07860.03880.28370.04870.3071-14.5613-29.4198-43.1878
61.302-0.2434-0.35350.07370.06740.1034-0.2552-0.545-0.2565-0.09440.18130.52710.26580.1523-0.0320.3749-0.051-0.09350.2510.06530.6231-21.381-51.367-50.59
70.0321-0.0835-0.03180.29040.00470.1989-0.12510.10480.3356-0.28720.38280.64950.2763-0.34650.00280.4746-0.0285-0.13440.45040.07270.4168-22.46-42.6105-61.6615
80.05440.23980.00860.7528-0.34350.5366-0.0353-0.00860.12210.03180.22090.52840.024-0.30570.040.23390.0311-0.02410.31640.1210.4482-23.5008-41.4718-47.6424
90.5236-0.4517-0.03721.38740.77081.1389-0.10850.04280.0318-0.13740.65131.4850.6329-0.70190.07940.3263-0.0793-0.13510.59840.28830.8505-34.829-40.0323-51.4239
100.19380.1470.10130.10950.06390.20750.16050.1457-0.2033-0.06120.51970.9358-0.1083-0.87160.21360.39310.1261-0.03180.69790.26460.7481-30.5272-32.209-51.87
110.27840.0586-0.19681.1034-0.34430.1295-0.00290.13060.0049-0.13720.08270.2213-0.0249-0.0751-00.30690.07350.01420.27390.04670.2754-12.4366-24.5026-47.5788
120.005-0.2720.18820.17670.23590.4305-0.0112-0.1049-0.02280.06570.0656-0.09460.03390.137800.30210.0490.04460.23570.02490.2185-0.7847-9.2052-33.728
130.01160.17530.23810.0740.12010.4990.01190.01390.0676-0.2076-0.0921-0.09750.0259-0.0498-00.28070.00880.01070.24160.00930.291-6.1-3.335-23.15
140.1472-0.15210.11720.1057-0.1090.0718-0.0316-0.4850.31440.2072-0.1197-0.0436-0.53160.225-00.37-0.10180.00930.4025-0.05680.39716.88716.15-4.246
151.0596-0.2157-0.5580.12860.05060.2563-0.1851-0.6960.37840.1315-0.12050.0462-0.80580.5621-0.06390.6866-0.2039-0.10510.3669-0.08320.502112.954930.13543.0768
160.094-0.07410.43170.48650.59221.2928-0.00830.05260.065-0.05540.0592-0.1714-0.10650.2317-00.2682-0.0070.01520.2740.01930.31847.51936.3387-7.088
170.57370.1051-0.05760.11990.07570.1248-0.27080.2080.80660.63630.0004-0.5373-0.48560.182-0.04550.6899-0.1928-0.25450.5485-0.070.964527.50628.432410.0677
180.87320.3120.21930.10870.26510.61820.0741-0.1723-0.4351-0.0305-0.0550.04010.1967-0.14250.03170.38230.03160.0230.24920.0250.31894.9884-16.2412-74.3374
190.498-0.34630.3140.2355-0.4510.7466-0.00720.1345-0.0517-0.00610.0463-0.04490.17370.103100.2481-0.050.02130.227-0.01930.2263-1.44817.321-47.674
200.14750.2515-0.09290.4421-0.03460.16-0.0867-0.1266-0.00470.08740.0887-0.0171-0.02310.0007-00.2125-0.0384-0.03340.24250.01540.21040.442631.6176-31.4635
210.5297-0.19440.23870.530.40550.2085-0.0734-0.03430.0631-0.02530.12010.05770.0478-0.042800.2536-0.02690.00870.20960.040.2239-11.459234.0524-29.0996
220.0883-0.12130.0650.1382-0.14980.0949-0.0380.08270.0692-0.20310.0820.20550.0492-0.2528-00.2309-0.0314-0.04210.21570.030.2841-20.41230.595-32.76
230.63220.1356-0.10370.6087-0.41280.2209-0.1055-0.21060.23250.14550.18660.1358-0.04420.18930.00460.25110.00920.01770.2434-0.01330.3525-21.502749.3618-25.6954
240.34410.1010.18911.13380.15670.3919-0.14930.03910.1324-0.02580.09690.24760.0516-0.08120.00920.21460.0182-0.01780.24160.05960.3782-25.884246.5571-32.6337
250.79220.07050.03930.51910.18260.0462-0.0999-0.0589-0.00670.00560.05660.4071-0.0482-0.3270.00250.25770.02970.03440.36280.06140.4797-34.886341.979-27.2643
260.8822-0.1723-0.31880.97120.31410.6692-0.02380.00990.037-0.04990.0160.11070.0691-0.06770.00150.1788-0.0253-0.02230.19660.02280.2191-17.754132.5904-34.0791
270.21210.262-0.07530.2991-0.15880.1011-0.0477-0.1598-0.2223-0.14650.0334-0.13910.0470.08800.23530.0135-0.00110.2430.03860.2521-0.992517.6252-27.6935
280.0544-0.10040.10530.21510.09120.1682-0.11950.12020.1101-0.00620.1477-0.06330.13380.168800.299-0.02380.00140.2472-0.04110.2442-1.501716.6493-47.0119
290.0665-0.0349-0.08550.07610.0620.0336-0.14810.2234-0.06710.1674-0.17180.00660.3912-0.0638-0.0020.4098-0.075-0.02930.2983-0.02280.3358-6.1717.657-52.451
300.0147-0.3359-0.30490.14170.39830.1052-0.0637-0.006-0.111-0.0625-0.03780.1516-0.13760.1318-00.3849-0.0180.02880.2804-0.03090.3288-9.0357.083-55.867
310.12710.1653-0.0940.1446-0.13250.0578-0.13890.1035-0.1157-0.23540.08380.1643-0.17720.041900.44210.0267-0.00820.3903-0.02860.28084.342-12.27-74.567
320.48080.23820.08830.3999-0.27790.2460.07010.3015-0.5819-0.309-0.0558-0.00330.71730.21780.05850.54230.0978-0.02410.267-0.06070.527410.8285-26.2454-81.5463
330.6420.22540.24180.21430.06910.37210.0454-0.38750.31080.05780.1841-0.3307-0.02740.1635-00.3683-0.0342-0.03220.43790.02770.383512.9378-7.2745-71.1214
34-0.1135-0.06760.13110.85370.41670.41430.10910.0917-0.1585-0.0889-0.22260.0413-0.1066-0.0827-00.2892-0.02680.01480.3035-0.01520.278-1.50391.9164-69.649
350.26370.1605-0.22840.1482-0.18820.16270.10510.4147-0.2765-0.6746-0.2822-0.53380.62480.3449-0.00080.58050.2310.15720.5912-0.04740.758623.64-22.6226-90.3407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 57 )
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 128 )
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 156 )
6X-RAY DIFFRACTION6chain 'A' and (resid 157 through 166 )
7X-RAY DIFFRACTION7chain 'A' and (resid 167 through 193 )
8X-RAY DIFFRACTION8chain 'A' and (resid 197 through 231)
9X-RAY DIFFRACTION9chain 'A' and (resid 232 through 259 )
10X-RAY DIFFRACTION10chain 'A' and (resid 260 through 284 )
11X-RAY DIFFRACTION11chain 'A' and (resid 285 through 359 )
12X-RAY DIFFRACTION12chain 'A' and (resid 360 through 397 )
13X-RAY DIFFRACTION13chain 'A' and (resid 398 through 415 )
14X-RAY DIFFRACTION14chain 'A' and (resid 416 through 429 )
15X-RAY DIFFRACTION15chain 'B' and (resid 9 through 37 )
16X-RAY DIFFRACTION16chain 'B' and (resid 38 through 135 )
17X-RAY DIFFRACTION17chain 'B' and (resid 136 through 157 )
18X-RAY DIFFRACTION18chain 'C' and (resid 3 through 30 )
19X-RAY DIFFRACTION19chain 'C' and (resid 31 through 57 )
20X-RAY DIFFRACTION20chain 'C' and (resid 58 through 91 )
21X-RAY DIFFRACTION21chain 'C' and (resid 92 through 128 )
22X-RAY DIFFRACTION22chain 'C' and (resid 129 through 146 )
23X-RAY DIFFRACTION23chain 'C' and (resid 147 through 191 )
24X-RAY DIFFRACTION24chain 'C' and ((resid 192 through 193) or (resid 197 through 231 ))
25X-RAY DIFFRACTION25chain 'C' and (resid 232 through 284 )
26X-RAY DIFFRACTION26chain 'C' and (resid 285 through 343 )
27X-RAY DIFFRACTION27chain 'C' and (resid 344 through 366 )
28X-RAY DIFFRACTION28chain 'C' and (resid 367 through 384 )
29X-RAY DIFFRACTION29chain 'C' and (resid 385 through 397 )
30X-RAY DIFFRACTION30chain 'C' and (resid 398 through 415 )
31X-RAY DIFFRACTION31chain 'C' and (resid 416 through 429 )
32X-RAY DIFFRACTION32chain 'D' and (resid 9 through 38 )
33X-RAY DIFFRACTION33chain 'D' and (resid 39 through 68 )
34X-RAY DIFFRACTION34chain 'D' and (resid 69 through 126 )
35X-RAY DIFFRACTION35chain 'D' and (resid 127 through 157 )

+
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