[English] 日本語
Yorodumi
- PDB-4wsu: The crystal structure of hemagglutinin from A/Taiwan/1/2013 in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wsu
TitleThe crystal structure of hemagglutinin from A/Taiwan/1/2013 in complex with 3'SLN
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Hemagglutinin / influenza virus / H6
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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
Similarity search - Function
Haemagglutinin, influenzavirus B / Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin ...Haemagglutinin, influenzavirus B / Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Hemagglutinin HA2 chain / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsYang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.
CitationJournal: J.Virol. / Year: 2015
Title: Structure and receptor binding preferences of recombinant hemagglutinins from avian and human h6 and h10 influenza a virus subtypes.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / database_PDB_caveat / entity / entity_src_gen / 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_mod_residue / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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.name / _chem_comp.type / _citation.journal_id_CSD / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_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 / _struct_asym.entity_id / _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 2.1Dec 27, 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 / struct_conn / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1 chain
C: Hemagglutinin HA1 chain
E: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
D: Hemagglutinin HA2 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,45218
Polymers174,4606
Non-polymers2,99312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32550 Å2
ΔGint-136 kcal/mol
Surface area60890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.978, 100.080, 135.239
Angle α, β, γ (deg.)90.00, 126.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13C
23E
14B
24D
15B
25F
16D
26F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROAA0 - 3245 - 329
21SERSERPROPROCB0 - 3245 - 329
12SERSERPROPROAA0 - 3245 - 329
22SERSERPROPROEC0 - 3245 - 329
13SERSERPROPROCB0 - 3245 - 329
23SERSERPROPROEC0 - 3245 - 329
14GLYGLYARGARGBD1 - 1701 - 170
24GLYGLYARGARGDE1 - 1701 - 170
15GLYGLYARGARGBD1 - 1701 - 170
25GLYGLYARGARGFF1 - 1701 - 170
16GLYGLYARGARGDE1 - 1701 - 170
26GLYGLYARGARGFF1 - 1701 - 170

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein Hemagglutinin HA1 chain


Mass: 37434.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: new identified strain A/Taiwan/2/2013(H6N1) / Source: (gene. exp.) Influenza A virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X246*PLUS
#2: Protein Hemagglutinin HA2 chain


Mass: 20718.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: new identified strain A/Taiwan/2/2013(H6N1) / Source: (gene. exp.) Influenza A virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X245*PLUS
#3: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / 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
#5: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.01M nickel chloride, 0.1 M Tris-HCl pH 8.5 and 20% (w/v) PEG 2000MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 54578 / % possible obs: 98.3 % / Redundancy: 3.4 % / Net I/σ(I): 20.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.7→49.94 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.906 / SU B: 27.571 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 1.045 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2779 5.1 %RANDOM
Rwork0.212 ---
obs0.214 51799 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.01 Å2
2--0.18 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11814 0 192 0 12006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912302
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211312
X-RAY DIFFRACTIONr_angle_refined_deg1.861.95716699
X-RAY DIFFRACTIONr_angle_other_deg1.068326011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35251479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38824.824597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.595152052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1661563
X-RAY DIFFRACTIONr_chiral_restr0.1020.21814
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213990
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022872
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9883.9725934
X-RAY DIFFRACTIONr_mcbond_other2.9863.9725933
X-RAY DIFFRACTIONr_mcangle_it4.7075.9587407
X-RAY DIFFRACTIONr_mcangle_other4.7075.9587408
X-RAY DIFFRACTIONr_scbond_it3.6124.4126368
X-RAY DIFFRACTIONr_scbond_other3.6124.4136369
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6666.4699293
X-RAY DIFFRACTIONr_long_range_B_refined7.77631.72413166
X-RAY DIFFRACTIONr_long_range_B_other7.77531.72713167
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A194000.03
12C194000.03
21A194040.03
22E194040.03
31C194090.03
32E194090.03
41B87040.08
42D87040.08
51B86990.08
52F86990.08
61D87240.08
62F87240.08
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 205 -
Rwork0.298 3497 -
obs--90.91 %
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)
10.9509-0.08430.14580.1024-0.04570.1081-0.08670.13340.041-0.04270.05020.0134-0.0123-0.00560.03650.0441-0.0233-0.020.1320.01660.022-50.971533.5682-1.5589
21.0638-0.06120.09150.0293-0.03620.0536-0.0147-0.04250.08370.00880.02040.0117-0.0249-0.0308-0.00570.02820.0178-0.00540.0392-0.02850.0834-59.92550.060127.7927
30.71280.18190.17780.06230.08070.1609-0.00390.02-0.15270.017-0.0049-0.01970.0305-0.02830.00880.0492-0.0338-0.01470.03350.01630.105-59.595715.184426.8476
43.908-0.02240.18650.1480.00310.1051-0.1177-0.0714-0.1110.02210.0644-0.0236-0.01810.00960.05330.05010.00220.00620.0663-0.00020.0486-3.641233.079122.0493
53.24840.96191.21680.34820.32620.5696-0.02270.1119-0.03470.00090.0405-0.00210.00320.0587-0.01780.0567-0.0039-0.00130.0409-0.02810.032-9.188442.870139.3591
63.1407-0.95671.60780.525-0.51110.8321-0.07060.02340.10890.08010.0037-0.0951-0.04130.00120.06680.06640.004-0.01380.03590.01850.0594-8.928422.558738.79
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 324
2X-RAY DIFFRACTION2C0 - 324
3X-RAY DIFFRACTION3E0 - 324
4X-RAY DIFFRACTION4B1 - 170
5X-RAY DIFFRACTION5D1 - 170
6X-RAY DIFFRACTION6F1 - 170

+
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