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- PDB-3zp0: INFLUENZA VIRUS (VN1194) H5 HA with LSTa -

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Basic information

Entry
Database: PDB / ID: 3zp0
TitleINFLUENZA VIRUS (VN1194) H5 HA with LSTa
Components(HEMAGGLUTININ) x 2
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / 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
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.51 Å
AuthorsLiu, J. / Stevens, D.J. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Virology / Year: 2013
Title: Changes in the Hemagglutinin of H5N1 Viruses During Human Infection - Influence on Receptor Binding.
Authors: Crusat, M. / Liu, J. / Palma, A.S. / Childs, R.A. / Liu, Y. / Wharton, S.A. / Lin, Y.P. / Coombs, P.J. / Martin, S.R. / Matrosovich, M. / Chen, Z. / Stevens, D.J. / Hien, V.M. / Thanh, T.T. ...Authors: Crusat, M. / Liu, J. / Palma, A.S. / Childs, R.A. / Liu, Y. / Wharton, S.A. / Lin, Y.P. / Coombs, P.J. / Martin, S.R. / Matrosovich, M. / Chen, Z. / Stevens, D.J. / Hien, V.M. / Thanh, T.T. / Nhu, L.N.T. / Nguyet, L.A. / Ha, D.Q. / van Doorn, H.R. / Hien, T.T. / Conradt, H.S. / Kiso, M. / Gamblin, S.J. / Chai, W. / Skehel, J.J. / Hay, A.J. / Farrar, J. / De Jong, M.D. / Feizi, T.
History
DepositionFeb 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation_author / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.name / _chem_comp.type / _citation_author.name / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
E: HEMAGGLUTININ
F: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5784
Polymers56,8852
Non-polymers6932
Water3,369187
1
E: HEMAGGLUTININ
F: HEMAGGLUTININ
hetero molecules

E: HEMAGGLUTININ
F: HEMAGGLUTININ
hetero molecules

E: HEMAGGLUTININ
F: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,73312
Polymers170,6556
Non-polymers2,0786
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area32400 Å2
ΔGint-120.9 kcal/mol
Surface area59950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.220, 101.220, 449.780
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
11F-2045-

HOH

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Components

#1: Protein HEMAGGLUTININ / H5 HA


Mass: 38494.801 Da / Num. of mol.: 1
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Organ (production host): EGG / Production host: GALLUS GALLUS (chicken) / References: UniProt: Q6DQ34
#2: Protein HEMAGGLUTININ / H5 HA


Mass: 18390.303 Da / Num. of mol.: 1
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Organ (production host): EGG / Production host: GALLUS GALLUS (chicken) / References: UniProt: Q6DQ34
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+2)][a-D-Neup5Ac]{}}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.: 1
Source method: isolated from a genetically manipulated source
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.89 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Type: DIAMOND / Wavelength: 0.9715
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9715 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 27704 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 14.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.2

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Processing

SoftwareName: REFMAC / Version: 5.5.0088 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.51→30 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.899 / SU B: 21.334 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2852 1401 5.1 %RANDOM
Rwork0.24166 ---
obs0.24385 26325 89.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.425 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.51→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3821 0 45 187 4053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224015
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.9655437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7065477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73125.202198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35915676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3071517
X-RAY DIFFRACTIONr_chiral_restr0.0680.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213042
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4521.52382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88723846
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.13331633
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9954.51591
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.482 26 -
Rwork0.358 328 -
obs--15.75 %
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)
10.32230.1166-0.05320.0827-0.19161.2971-0.13070.037-0.021-0.1028-0.0453-0.06960.30960.44650.1760.19280.12370.10870.20010.05990.1285-32.14420.0183.162
20.5743-0.24460.8490.132-0.33033.6067-0.1172-0.0789-0.00370.02780.0111-0.01810.15150.02020.10610.10120.03140.0310.10930.03650.2121-39.89623.83252.829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E5 - 325
2X-RAY DIFFRACTION2F1 - 160

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