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- PDB-6cf5: Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza vir... -

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Basic information

Entry
Database: PDB / ID: 6cf5
TitleCrystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in complex with small molecule N-Cyclohexyltaurine
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / Glycoprotein / Ectodomain / N-glycosylation
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion membrane ...viral budding from plasma membrane / 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 / virion membrane / membrane / identical protein binding
Similarity search - Function
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 ...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
DI(HYDROXYETHYL)ETHER / Hemagglutinin / Hemagglutinin / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsWilson, I.A. / Kadam, R.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: A small-molecule fragment that emulates binding of receptor and broadly neutralizing antibodies to influenza A hemagglutinin.
Authors: Kadam, R.U. / Wilson, I.A.
History
DepositionFeb 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 2, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)178,97028
Polymers175,0886
Non-polymers3,88222
Water23,9241328
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34250 Å2
ΔGint-86 kcal/mol
Surface area61520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.583, 232.980, 72.626
Angle α, β, γ (deg.)90.00, 118.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin /


Mass: 37948.020 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EP31, UniProt: Q6DQ33*PLUS
#2: Protein Hemagglutinin /


Mass: 20414.504 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6DQ18, UniProt: A8UDR1*PLUS

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Sugars , 2 types, 6 molecules

#3: 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.: 3 / 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: 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.: 3 / 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

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Non-polymers , 4 types, 1344 molecules

#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1328 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM of CHES, pH 9.5 and 40% v/v PEG600, 20 degree celsiu

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 131851 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.02 / Rsym value: 0.04 / Net I/σ(I): 29.3
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 6.9 / Num. unique obs: 6021 / CC1/2: 0.97 / Rpim(I) all: 0.08 / Rsym value: 0.16 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FQI

4fqi


Resolution: 2.04→37.583 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.27
RfactorNum. reflection% reflection
Rfree0.2215 6500 4.93 %
Rwork0.1914 --
obs0.1929 131782 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.04→37.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11950 0 252 1331 13533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312543
X-RAY DIFFRACTIONf_angle_d0.59716974
X-RAY DIFFRACTIONf_dihedral_angle_d13.5447572
X-RAY DIFFRACTIONf_chiral_restr0.0451815
X-RAY DIFFRACTIONf_plane_restr0.0032198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0372-2.06030.26011830.23073614X-RAY DIFFRACTION85
2.0603-2.08460.25822140.23293845X-RAY DIFFRACTION91
2.0846-2.110.27031930.2323889X-RAY DIFFRACTION92
2.11-2.13670.28771870.23644078X-RAY DIFFRACTION95
2.1367-2.16480.25262620.23033933X-RAY DIFFRACTION94
2.1648-2.19440.27112210.23244160X-RAY DIFFRACTION97
2.1944-2.22580.26411660.22984196X-RAY DIFFRACTION99
2.2258-2.2590.27031650.22744257X-RAY DIFFRACTION99
2.259-2.29430.26952110.22454188X-RAY DIFFRACTION99
2.2943-2.33190.24272530.22284248X-RAY DIFFRACTION100
2.3319-2.37210.25592110.21014197X-RAY DIFFRACTION100
2.3721-2.41520.24192740.2084229X-RAY DIFFRACTION100
2.4152-2.46170.2362400.20544182X-RAY DIFFRACTION100
2.4617-2.51190.26242280.20814250X-RAY DIFFRACTION100
2.5119-2.56650.25031860.21384244X-RAY DIFFRACTION100
2.5665-2.62620.23762390.21084195X-RAY DIFFRACTION100
2.6262-2.69190.24582560.20494229X-RAY DIFFRACTION100
2.6919-2.76460.22322640.20284201X-RAY DIFFRACTION100
2.7646-2.8460.21141520.19194302X-RAY DIFFRACTION100
2.846-2.93780.23052070.2044227X-RAY DIFFRACTION100
2.9378-3.04270.2212180.19384277X-RAY DIFFRACTION100
3.0427-3.16450.21651540.19334336X-RAY DIFFRACTION100
3.1645-3.30850.22962300.18434223X-RAY DIFFRACTION100
3.3085-3.48280.20762360.18664253X-RAY DIFFRACTION100
3.4828-3.70080.19451650.16714270X-RAY DIFFRACTION100
3.7008-3.98620.19682540.1644219X-RAY DIFFRACTION100
3.9862-4.38680.17292220.15644259X-RAY DIFFRACTION100
4.3868-5.02040.18542260.16094255X-RAY DIFFRACTION100
5.0204-6.32020.21462320.18044253X-RAY DIFFRACTION100
6.3202-37.58940.212510.18324273X-RAY DIFFRACTION100

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