[English] 日本語
Yorodumi
- PDB-5e5w: Hemagglutinin-esterase-fusion mutant structure of influenza D virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e5w
TitleHemagglutinin-esterase-fusion mutant structure of influenza D virus
Components(Hemagglutinin- ...) x 2
KeywordsHYDROLASE / influenza virus / HEF
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: 2.4 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _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_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 2.2Oct 16, 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)132,20114
Polymers126,2554
Non-polymers5,94510
Water9,800544
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)199,03121
Polymers189,3836
Non-polymers9,64815
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 area45470 Å2
ΔGint76 kcal/mol
Surface area67100 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)197,57121
Polymers189,3836
Non-polymers8,18915
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area42220 Å2
ΔGint51 kcal/mol
Surface area67580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.335, 164.335, 164.335
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: 16670.598 Da / Num. of mol.: 2 / Fragment: UNP residues 456-612
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 ascovirus 1a / References: UniProt: K9LG83

-
Sugars , 4 types, 10 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.: 4 / 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 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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, 544 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.01 %
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) PEG1500

-
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, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49.55 Å / Num. obs: 57383 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 2.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.769 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLC

1flc


Resolution: 2.4→49.55 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 2913 5.08 %
Rwork0.205 --
obs0.207 57383 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8700 0 395 544 9639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0189330
X-RAY DIFFRACTIONf_angle_d1.48812654
X-RAY DIFFRACTIONf_dihedral_angle_d15.283429
X-RAY DIFFRACTIONf_chiral_restr0.0831449
X-RAY DIFFRACTIONf_plane_restr0.0051602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4027-2.44210.33821520.25332589X-RAY DIFFRACTION100
2.4421-2.48420.33921310.25022569X-RAY DIFFRACTION100
2.4842-2.52940.29381410.24172593X-RAY DIFFRACTION100
2.5294-2.5780.27531440.232584X-RAY DIFFRACTION100
2.578-2.63060.32041280.23572566X-RAY DIFFRACTION100
2.6306-2.68780.3171340.2332589X-RAY DIFFRACTION100
2.6878-2.75040.31091200.22662599X-RAY DIFFRACTION100
2.7504-2.81910.28241560.22852581X-RAY DIFFRACTION100
2.8191-2.89530.31551440.22882595X-RAY DIFFRACTION100
2.8953-2.98050.26721620.22372602X-RAY DIFFRACTION100
2.9805-3.07670.26431290.23012567X-RAY DIFFRACTION100
3.0767-3.18670.29271300.23022620X-RAY DIFFRACTION100
3.1867-3.31420.2681570.22362571X-RAY DIFFRACTION100
3.3142-3.4650.29171470.20082593X-RAY DIFFRACTION100
3.465-3.64770.20271380.20062596X-RAY DIFFRACTION100
3.6477-3.87610.21261230.18642618X-RAY DIFFRACTION100
3.8761-4.17530.24651380.17762600X-RAY DIFFRACTION99
4.1753-4.59520.20791300.16832603X-RAY DIFFRACTION99
4.5952-5.25940.19981290.1642620X-RAY DIFFRACTION99
5.2594-6.62380.24551250.19722606X-RAY DIFFRACTION98
6.6238-49.55940.22711550.20632609X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -7.0205 Å / Origin y: -2.1715 Å / Origin z: -42.6502 Å
111213212223313233
T0.195 Å2-0.0037 Å20.0025 Å2-0.1965 Å20.0107 Å2--0.2109 Å2
L0.0543 °2-0.02 °20.0296 °2-0.0965 °2-0.0532 °2--0.0339 °2
S0.0006 Å °-0.0137 Å °-0.01 Å °0.0079 Å °-0.0073 Å °-0.0194 Å °-0.0143 Å °0.0238 Å °0 Å °
Refinement TLS groupSelection details: ALL

+
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