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- PDB-4eda: Structures of monomeric hemagglutinin and its complex with an Fab... -

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Basic information

Entry
Database: PDB / ID: 4eda
TitleStructures of monomeric hemagglutinin and its complex with an Fab fragment of a neutralizing antibody that binds to H1 subtype influenza viruses: molecular basis of infectivity of 2009 pandemic H1N1 influenza A viruses
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / influenza virus / haemagglutinin / conformation / antibody
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
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 / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsKim, K.H. / Cho, K.J. / Lee, J.H. / Park, Y.H. / Khan, T.G. / Lee, J.Y. / Kang, S.H. / Alam, I.
CitationJournal: J.Gen.Virol. / Year: 2013
Title: Insight into structural diversity of influenza virus haemagglutinin
Authors: Cho, K.J. / Lee, J.H. / Hong, K.W. / Kim, S.H. / Park, Y. / Lee, J.Y. / Kang, S. / Kim, S. / Yang, J.H. / Kim, E.K. / Seok, J.H. / Unzai, S. / Park, S.Y. / Saelens, X. / Kim, C.J. / Lee, J.Y. ...Authors: Cho, K.J. / Lee, J.H. / Hong, K.W. / Kim, S.H. / Park, Y. / Lee, J.Y. / Kang, S. / Kim, S. / Yang, J.H. / Kim, E.K. / Seok, J.H. / Unzai, S. / Park, S.Y. / Saelens, X. / Kim, C.J. / Lee, J.Y. / Kang, C. / Oh, H.B. / Chung, M.S. / Kim, K.H.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references / Derived calculations
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,10410
Polymers116,3704
Non-polymers1,7346
Water1,13563
1
A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0525
Polymers58,1852
Non-polymers8673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-17 kcal/mol
Surface area24390 Å2
MethodPISA
2
C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0525
Polymers58,1852
Non-polymers8673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-2 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.126, 208.126, 65.765
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Hemagglutinin /


Mass: 37341.082 Da / Num. of mol.: 2 / Fragment: HA1 SUBUNIT, UNP residues 18-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Korea/01/2009 H1N1 / Gene: HA / Plasmid: pAcGP67A / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C5MQE6
#2: Protein Hemagglutinin /


Mass: 20844.113 Da / Num. of mol.: 2 / Fragment: HA2 SUBUNIT, UNP residues 345-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Korea/01/2009 H1N1 / Gene: HA / Plasmid: pAcGP67A / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C5MQE6
#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: isolated from a genetically manipulated source
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-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.53 Å3/Da / Density % sol: 65.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES (pH7.5), 20% PEG 3350, 200mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.085
ReflectionResolution: 2.7→50 Å / Num. all: 44988 / Num. obs: 44808 / % possible obs: 99.6 %
Reflection shellResolution: 2.7→2.8 Å / % possible all: 95.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.701→49.99 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7263 / σ(F): 1.38 / Phase error: 34 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2892 2265 5.05 %RANDOM
Rwork0.2373 ---
obs0.2397 44808 99.51 %-
all-45029 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.247 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 163.25 Å2 / Biso mean: 86.5383 Å2 / Biso min: 34.21 Å2
Baniso -1Baniso -2Baniso -3
1-13.3152 Å2-0 Å2-0 Å2
2--13.3152 Å20 Å2
3----26.6304 Å2
Refinement stepCycle: LAST / Resolution: 2.701→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7050 0 112 63 7225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077324
X-RAY DIFFRACTIONf_angle_d1.219905
X-RAY DIFFRACTIONf_chiral_restr0.0761102
X-RAY DIFFRACTIONf_plane_restr0.0051263
X-RAY DIFFRACTIONf_dihedral_angle_d18.1462700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7023-2.7610.38761280.32052506263490
2.761-2.82520.32881460.30922574272093
2.8252-2.89580.32861480.29882646279495
2.8958-2.97410.32591500.29062642279295
2.9741-3.06160.28731390.27322638277795
3.0616-3.16040.29991260.2672692281896
3.1604-3.27330.30631290.25752656278595
3.2733-3.40430.2981500.25112631278195
3.4043-3.55920.30011250.23882662278796
3.5592-3.74670.26211400.23252682282295
3.7467-3.98130.25541630.22492648281194
3.9813-4.28840.31341600.21872648280894
4.2884-4.71940.29721250.21132706283196
4.7194-5.4010.26631390.20782691283095
5.401-6.79980.29881430.24182706284995
6.7998-41.35530.271490.22032791294095

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