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- PDB-6cfg: Crystal structure of the A/Vietnam/1203/2004 (H5N1) influenza vir... -

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Basic information

Entry
Database: PDB / ID: 6cfg
TitleCrystal structure of the A/Vietnam/1203/2004 (H5N1) influenza virus hemagglutinin in complex with small molecule JNJ4796
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 / membrane
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
Chem-EZ7 / DI(HYDROXYETHYL)ETHER / Hemagglutinin / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsKadam, R.U. / Wilson, I.A.
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: Science / Year: 2019
Title: A small-molecule fusion inhibitor of influenza virus is orally active in mice.
Authors: van Dongen, M.J.P. / Kadam, R.U. / Juraszek, J. / Lawson, E. / Brandenburg, B. / Schmitz, F. / Schepens, W.B.G. / Stoops, B. / van Diepen, H.A. / Jongeneelen, M. / Tang, C. / Vermond, J. / ...Authors: van Dongen, M.J.P. / Kadam, R.U. / Juraszek, J. / Lawson, E. / Brandenburg, B. / Schmitz, F. / Schepens, W.B.G. / Stoops, B. / van Diepen, H.A. / Jongeneelen, M. / Tang, C. / Vermond, J. / van Eijgen-Obregoso Real, A. / Blokland, S. / Garg, D. / Yu, W. / Goutier, W. / Lanckacker, E. / Klap, J.M. / Peeters, D.C.G. / Wu, J. / Buyck, C. / Jonckers, T.H.M. / Roymans, D. / Roevens, P. / Vogels, R. / Koudstaal, W. / Friesen, R.H.E. / Raboisson, P. / Dhanak, D. / Goudsmit, J. / Wilson, I.A.
History
DepositionFeb 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 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 / 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_struct_special_symmetry / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2978
Polymers58,3632
Non-polymers1,9356
Water1,67593
1
A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,89224
Polymers175,0886
Non-polymers5,80518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area33060 Å2
ΔGint-90 kcal/mol
Surface area63640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.197, 102.197, 454.053
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-335-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 37948.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Strain: A/Vietnam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EP31
#2: Protein Hemagglutinin


Mass: 20414.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Strain: A/Vietnam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6DQ18, UniProt: A8UDR1*PLUS

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Sugars , 2 types, 4 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.: 2 / 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
#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


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

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Non-polymers , 3 types, 95 molecules

#5: Chemical ChemComp-EZ7 / N-[2-(2-{4-[(R)-(2-methyl-2H-tetrazol-5-yl)(phenyl)methyl]piperazine-1-carbonyl}pyridin-4-yl)-1,3-benzoxazol-5-yl]acetamide


Mass: 537.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27N9O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.91 Å3/Da / Density % sol: 68.54 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium sulfate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 40297 / % possible obs: 99.2 % / Redundancy: 9.8 % / Biso Wilson estimate: 46 Å2 / CC1/2: 0.97 / Rpim(I) all: 0.02 / Rsym value: 0.08 / Net I/σ(I): 26.1
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1773 / CC1/2: 0.88 / Rpim(I) all: 0.28 / Rsym value: 0.82 / % possible all: 89.5

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FQI

4fqi


Resolution: 2.32→40.399 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.33
RfactorNum. reflection% reflection
Rfree0.2413 2036 5.11 %
Rwork0.2041 --
obs0.206 39877 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.32→40.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 131 93 4214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084249
X-RAY DIFFRACTIONf_angle_d0.8945767
X-RAY DIFFRACTIONf_dihedral_angle_d13.0982550
X-RAY DIFFRACTIONf_chiral_restr0.052618
X-RAY DIFFRACTIONf_plane_restr0.005748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.3740.3375990.33522327X-RAY DIFFRACTION92
2.374-2.43330.34091330.30522449X-RAY DIFFRACTION98
2.4333-2.49910.37551450.29172486X-RAY DIFFRACTION100
2.4991-2.57260.321520.2642470X-RAY DIFFRACTION100
2.5726-2.65570.30621170.2542520X-RAY DIFFRACTION100
2.6557-2.75060.25811380.24232522X-RAY DIFFRACTION100
2.7506-2.86070.28591510.24392497X-RAY DIFFRACTION100
2.8607-2.99080.37851600.25442483X-RAY DIFFRACTION100
2.9908-3.14840.271090.23072562X-RAY DIFFRACTION100
3.1484-3.34560.22581370.22582529X-RAY DIFFRACTION100
3.3456-3.60380.26081380.22482538X-RAY DIFFRACTION100
3.6038-3.96620.20321310.17962567X-RAY DIFFRACTION100
3.9662-4.53940.16961360.15012566X-RAY DIFFRACTION100
4.5394-5.71660.19471540.16262602X-RAY DIFFRACTION100
5.7166-40.40520.24251360.18722723X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.4849 Å / Origin y: -41.3492 Å / Origin z: 23.4752 Å
111213212223313233
T0.5001 Å2-0.0883 Å2-0.0751 Å2-0.3371 Å20.0399 Å2--0.4578 Å2
L0.6349 °2-0.1232 °20.1848 °2-0.5795 °2-0.3189 °2--4.256 °2
S-0.0734 Å °0.2484 Å °0.1336 Å °-0.1582 Å °-0.03 Å °0.0115 Å °-0.818 Å °0.3608 Å °0.0916 Å °
Refinement TLS groupSelection details: all

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