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- PDB-4lkj: The structure of hemagglutinin L226Q mutant (H3 numbering) from a... -

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Entry
Database: PDB / ID: 4lkj
TitleThe structure of hemagglutinin L226Q mutant (H3 numbering) from a avian-origin H7N9 influenza virus (A/Anhui/1/2013) in complex with avian receptor analog 3'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
3'-sialyl-N-acetyllactosamine / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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 2.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: hemagglutinin
B: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9826
Polymers53,6442
Non-polymers1,3384
Water57632
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)164,94618
Polymers160,9316
Non-polymers4,01512
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 area36630 Å2
ΔGint-112 kcal/mol
Surface area57870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.909, 116.909, 297.076
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-603-

HOH

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Components

#1: Protein hemagglutinin


Mass: 34210.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Anhui/1/2013 / Plasmid: pFastbac1 / Cell line (production host): HI5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: V5IRV5*PLUS
#2: Protein hemagglutinin


Mass: 19433.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Anhui/1/2013 / Plasmid: pFastbac1 / Cell line (production host): HI5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: V5IRV2*PLUS
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-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*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-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.: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN WHICH DERIVED FROM STRAIN A/ANHUI/1/2013 DOES NOT ...THE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN WHICH DERIVED FROM STRAIN A/ANHUI/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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 16%(w/v) Polyethylene glycol 3350, 0.2M lithium sulfate, 0.1M Tris, pH 8.5, 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: Jun 28, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.798→50 Å / Num. all: 19702 / Num. obs: 19499 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 72.22 Å2
Reflection shellResolution: 2.8→2.9 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: 2.798→37.781 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7481 / SU ML: 0.45 / σ(F): 1.35 / Phase error: 31.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2849 993 5.09 %RANDOM
Rwork0.237 ---
all0.2394 19491 --
obs0.2394 19491 98.96 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.668 Å2 / ksol: 0.252 e/Å3
Displacement parametersBiso max: 220.83 Å2 / Biso mean: 96.2352 Å2 / Biso min: 31.51 Å2
Baniso -1Baniso -2Baniso -3
1-4.9479 Å2-0 Å2-0 Å2
2--4.9479 Å20 Å2
3----9.8959 Å2
Refinement stepCycle: LAST / Resolution: 2.798→37.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 88 32 3880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053929
X-RAY DIFFRACTIONf_angle_d0.9435306
X-RAY DIFFRACTIONf_chiral_restr0.201585
X-RAY DIFFRACTIONf_plane_restr0.004694
X-RAY DIFFRACTIONf_dihedral_angle_d18.0391456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7976-2.94510.4061300.329826262756100
2.9451-3.12950.39051680.318826112779100
3.1295-3.3710.35861330.29426472780100
3.371-3.70990.31751390.253926452784100
3.7099-4.24620.26481510.2272618276999
4.2462-5.34730.25171420.19072624276697
5.3473-37.78440.24181300.22412727285797
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)
10.72880.28590.15650.85480.29481.8928-0.07660.0124-0.0445-0.02510.0644-0.10120.02810.132-00.50180.0218-0.02950.4368-0.00660.5939-52.135713.7409-0.975
21.53421.63190.19722.0225-0.22790.7385-0.45980.45680.064-0.97680.52250.43910.5720.221800.83-0.0452-0.05410.71540.03920.7197-59.965411.8511-31.3283
30.2932-0.01640.35930.2931-0.30350.6860.09870.2452-0.1-0.66720.0380.4318-0.4621-0.004700.9362-0.1654-0.17940.62590.21050.8508-59.623523.4512-35.4241
41.89451.50140.59042.14220.92670.6807-0.2940.39550.3202-0.58650.21120.56150.01060.150900.6387-0.0326-0.09450.54460.09080.7722-59.453217.0728-24.0078
50.4478-0.0646-0.21180.69250.6310.58780.09710.0716-0.18150.189-0.2341-0.1906-0.0006-0.1744-00.499-0.030.0270.4312-0.05580.5894-49.879214.37318.1553
60.314-0.3042-0.01740.34880.1890.2428-0.2964-0.57030.14920.06550.20980.08740.0292-0.3896-0.00060.5330.1074-0.06230.7071-0.08130.3954-43.601324.406330.3713
70.86290.3325-0.17460.171-0.22140.4470.1496-0.8661-0.31040.6714-0.3386-0.54030.0250.92790.00451.5935-0.1332-0.34771.53750.22660.8082-45.750420.210852.1725
80.86150.341-0.61260.2317-0.19860.4409-0.3352-0.3336-0.20180.0284-0.2089-0.1061.2099-0.5081-0.0391.1285-0.0619-0.07570.87440.19510.7087-55.176115.986340.8064
90.5226-0.776-0.37351.53310.33970.3227-0.16420.4875-0.2618-0.13270.0448-0.1201-0.073-0.542-0.00420.64870.01550.07060.5350.03250.5823-54.653620.7271.0567
100.7707-0.45980.76720.4459-0.42140.82-0.0566-0.16610.09260.03740.0882-0.15380.1810.05100.4641-0.0131-0.06780.3981-0.03620.4617-53.620129.388226.4972
110.79740.49280.09660.7112-0.07390.0493-0.2525-1.4956-0.12341.72020.1994-0.1662-0.79991.06830.01651.85970.1581-0.12951.97380.23810.581-52.464420.742865.2972
120.05110.10360.0520.17050.10890.0541-1.39050.00750.76580.3620.7921.38890.63260.2236-0.00621.71490.2989-0.02011.85690.2231.0264-59.719219.756270.7914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:122)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 123:175)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 176:204)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 205:259)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 260:299)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 300:316)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 323:352)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 353:376)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 377:395)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 396:446)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 447:474)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 475:490)

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