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- PDB-7t1v: Crystal structure of an equine H7 hemagglutinin from A/equine/NY/... -

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Basic information

Entry
Database: PDB / ID: 7t1v
TitleCrystal structure of an equine H7 hemagglutinin from A/equine/NY/49/73 (H7N7) in complex with 3'-GcLN
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / H7 / RECEPTOR SPECIFICITY
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: J.Virol. / Year: 2022
Title: N -Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses.
Authors: Spruit, C.M. / Zhu, X. / Tomris, I. / Rios-Carrasco, M. / Han, A.X. / Broszeit, F. / van der Woude, R. / Bouwman, K.M. / Luu, M.M.T. / Matsuno, K. / Sakoda, Y. / Russell, C.A. / Wilson, I.A. ...Authors: Spruit, C.M. / Zhu, X. / Tomris, I. / Rios-Carrasco, M. / Han, A.X. / Broszeit, F. / van der Woude, R. / Bouwman, K.M. / Luu, M.M.T. / Matsuno, K. / Sakoda, Y. / Russell, C.A. / Wilson, I.A. / Boons, G.J. / de Vries, R.P.
History
DepositionDec 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)180,04715
Polymers176,2836
Non-polymers3,7649
Water14,592810
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,77815
Polymers176,2836
Non-polymers4,4959
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area34330 Å2
ΔGint-140 kcal/mol
Surface area57420 Å2
MethodPISA
2
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
hetero molecules

C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
hetero molecules

C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,68215
Polymers176,2836
Non-polymers3,3999
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area35710 Å2
ΔGint-143 kcal/mol
Surface area57700 Å2
MethodPISA
3
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules

E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules

E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,68215
Polymers176,2836
Non-polymers3,3999
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area33460 Å2
ΔGint-136 kcal/mol
Surface area58590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.753, 112.753, 130.187
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-795-

HOH

21B-235-

HOH

31B-243-

HOH

41D-243-

HOH

51D-252-

HOH

61F-202-

HOH

71F-205-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
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
11ASPASPPROPROAA11 - 3244 - 318
21ASPASPPROPROCC11 - 3244 - 318
12ASPASPPROPROAA11 - 3244 - 318
22ASPASPPROPROEE11 - 3244 - 318
13GLYGLYARGARGBB1 - 1701 - 170
23GLYGLYARGARGDD1 - 1701 - 170
14GLYGLYARGARGBB1 - 1701 - 170
24GLYGLYARGARGFF1 - 1701 - 170
15ASPASPPROPROCC11 - 3244 - 318
25ASPASPPROPROEE11 - 3244 - 318
16GLYGLYARGARGDD1 - 1701 - 170
26GLYGLYARGARGFF1 - 1701 - 170

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain


Mass: 37227.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/equine/New York/49/1973(H7N7))
Strain: A/equine/New York/49/1973(H7N7) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A348FV55
#2: Protein Hemagglutinin HA2 chain


Mass: 21533.803 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/equine/New York/49/1973(H7N7))
Strain: A/equine/New York/49/1973(H7N7) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A348FV55

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Sugars , 5 types, 9 molecules

#3: Polysaccharide N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 690.603 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Gca2-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Gc]{}}}LINUCSPDB-CARE
#4: 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: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 487.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Gca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Gc]{}}LINUCSPDB-CARE
#6: 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: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: 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 / Feature type: SUBJECT OF INVESTIGATION
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 , 1 types, 810 molecules

#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 810 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 32% (w/v) polyethylene glycol 400 and 0.1 M CAPS, pH 10

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.05→50.01 Å / Num. obs: 116123 / % possible obs: 99.9 % / Redundancy: 9.4 % / CC1/2: 0.99 / Rpim(I) all: 0.032 / Rrim(I) all: 0.101 / Rsym value: 0.095 / Net I/σ(I): 16.1
Reflection shellResolution: 2.05→2.09 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 5442 / CC1/2: 0.7 / Rpim(I) all: 0.34 / Rsym value: 0.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N5A

6n5a


Resolution: 2.05→50.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.662 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 5856 5 %RANDOM
Rwork0.2169 ---
obs0.2183 110263 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 307.97 Å2 / Biso mean: 69.363 Å2 / Biso min: 16.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20.46 Å20 Å2
2--0.92 Å20 Å2
3----2.98 Å2
Refinement stepCycle: final / Resolution: 2.05→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11514 0 250 810 12574
Biso mean--64.87 48.18 -
Num. residues----1455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912010
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211142
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.96216218
X-RAY DIFFRACTIONr_angle_other_deg1.4325684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33951443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42224.85600
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.054152082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5311575
X-RAY DIFFRACTIONr_chiral_restr0.0840.21757
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213670
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022833
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A368680.09
12C368680.09
21A350100.14
22E350100.14
31B174320.11
32D174320.11
41B174060.12
42F174060.12
51C353640.13
52E353640.13
61D185020.03
62F185020.03
LS refinement shellResolution: 2.05→2.098 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.32 338 -
Rwork0.341 7586 -
obs--91.47 %

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