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- PDB-4lkh: The structure of hemagglutinin from a avian-origin H7N9 influenza... -

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Basic information

Entry
Database: PDB / ID: 4lkh
TitleThe structure of hemagglutinin from a avian-origin H7N9 influenza virus (A/Shanghai/1/2013) in complex with human receptor analog 6'SLNLN
Components(hemagglutinin) x 2
KeywordsVIRAL PROTEIN / homotrimer / virus attachment / membrane fusion
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / 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
Haemagglutinin, influenzavirus 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 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
N-acetyl-alpha-neuraminic acid / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.099 Å
AuthorsShi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. ...Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F.
CitationJournal: Science / Year: 2013
Title: Structures and receptor binding of hemagglutinins from human-infecting H7N9 influenza viruses
Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / ...Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F.
History
DepositionJul 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hemagglutinin
B: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0936
Polymers54,1202
Non-polymers9734
Water00
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)165,28018
Polymers162,3616
Non-polymers2,91912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area35770 Å2
ΔGint-145 kcal/mol
Surface area57290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.398, 116.398, 294.636
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein hemagglutinin


Mass: 34485.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/SHANGHAI/1/2013 / Plasmid: pFastbac1 / Cell line (production host): HI5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: V5IRV0*PLUS
#2: Protein hemagglutinin


Mass: 19634.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/SHANGHAI/1/2013 / Plasmid: pFastbac1 / Cell line (production host): HI5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: V5IRU7*PLUS
#3: 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.: 3
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
#4: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY
Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN WHICH DERIVED FROM STRAIN A/SHANGHAI/1/2013 DOES ...THE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN WHICH DERIVED FROM STRAIN A/SHANGHAI/1/2013 DOES NOT CURRENTLY EXIST.

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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: 3.55 Å3/Da / Density % sol: 65.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M ammonium citrate tribasic, 20%(w/v) Polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.099→50 Å / Num. all: 14322 / Num. obs: 14311 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 80.04 Å2
Reflection shellResolution: 3.1→3.21 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DJ6

4dj6


Resolution: 3.099→47.688 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 716 5.01 %RANDOM
Rwork0.2167 ---
all0.2186 14301 --
obs0.2186 14301 99.67 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.867 Å2 / ksol: 0.287 e/Å3
Displacement parametersBiso max: 221.94 Å2 / Biso mean: 108.9378 Å2 / Biso min: 37.57 Å2
Baniso -1Baniso -2Baniso -3
1-11.7291 Å20 Å20 Å2
2--11.7291 Å2-0 Å2
3----23.4582 Å2
Refinement stepCycle: LAST / Resolution: 3.099→47.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 63 0 3856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033934
X-RAY DIFFRACTIONf_angle_d0.7615306
X-RAY DIFFRACTIONf_chiral_restr0.049577
X-RAY DIFFRACTIONf_plane_restr0.002698
X-RAY DIFFRACTIONf_dihedral_angle_d16.1921450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0995-3.33870.34691520.29812646279899
3.3387-3.67460.28551450.247626782823100
3.6746-4.20610.25451480.201926972845100
4.2061-5.29810.23761290.183227342863100
5.2981-47.69370.23361420.218128302972100
Refinement TLS params.Method: refined / Origin x: 11.1634 Å / Origin y: 11.7624 Å / Origin z: 57.4185 Å
111213212223313233
T0.4317 Å2-0.0216 Å2-0.0426 Å2-0.4206 Å2-0.0056 Å2--0.5723 Å2
L1.1357 °20.1626 °2-0.0582 °2-0.994 °2-0.1667 °2--0.1174 °2
S0.0436 Å °0.0836 Å °0.1991 Å °0.0385 Å °0.0356 Å °-0.0183 Å °-0.1972 Å °0.01 Å °0 Å °
Refinement TLS groupSelection details: ALL

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