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- PDB-4gxx: Crystal structure of the "avianized" 1918 influenza virus hemaggl... -

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Basic information

Entry
Database: PDB / ID: 4gxx
TitleCrystal structure of the "avianized" 1918 influenza virus hemagglutinin
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / viral fusion protein / virus attachment and entry
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion 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 / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsEkiert, D.C. / Wilson, I.A.
CitationJournal: Plos Pathog. / Year: 2012
Title: Influenza Human Monoclonal Antibody 1F1 Interacts with Three Major Antigenic Sites and Residues Mediating Human Receptor Specificity in H1N1 Viruses.
Authors: Tsibane, T. / Ekiert, D.C. / Krause, J.C. / Martinez, O. / Crowe, J.E. / Wilson, I.A. / Basler, C.F.
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references / Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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_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 / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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

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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)172,85814
Polymers169,5066
Non-polymers3,3528
Water16,159897
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32280 Å2
ΔGint-90 kcal/mol
Surface area60210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.790, 241.510, 72.030
Angle α, β, γ (deg.)90.00, 119.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain / Hemagglutinin receptor binding subunit


Mass: 36408.785 Da / Num. of mol.: 3 / Fragment: UNP residues 18-344 / Mutation: D190E,D225G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/1918 H1N1 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High5 / References: UniProt: Q9WFX3
#2: Protein Hemagglutinin HA2 chain / Hemagglutinin membrane fusion subunit


Mass: 20093.121 Da / Num. of mol.: 3 / Fragment: UNP residues 345-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/1918 H1N1 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High5 / References: UniProt: Q9WFX3

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Sugars , 4 types, 8 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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.: 5
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

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Non-polymers , 1 types, 897 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 897 / 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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris, pH 8.0, 40% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. obs: 193879 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 51.5 Å2 / Rsym value: 0.09 / Net I/σ(I): 15.9
Reflection shellResolution: 1.799→1.9 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.57 / % possible all: 92.4

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Processing

Software
NameClassification
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RUZ

1ruz


Resolution: 1.799→35.895 Å / Occupancy max: 1 / Occupancy min: 0.03 / SU ML: 0.22 / σ(F): 1.33 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 9533 5.04 %RANDOM
Rwork0.1803 179611 --
obs0.1817 189144 96.44 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.9 Å2 / Biso mean: 51.5151 Å2 / Biso min: 20.4 Å2
Refinement stepCycle: LAST / Resolution: 1.799→35.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11631 0 220 897 12748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112378
X-RAY DIFFRACTIONf_angle_d1.26616822
X-RAY DIFFRACTIONf_chiral_restr0.0741845
X-RAY DIFFRACTIONf_plane_restr0.0062170
X-RAY DIFFRACTIONf_dihedral_angle_d18.0674577
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.799-1.8190.34392200.34544254447470
1.819-1.84040.37332600.34255062532280
1.8404-1.86280.36392820.33175226550885
1.8628-1.88640.34722920.32915568586089
1.8864-1.91120.36552890.32295756604594
1.9112-1.93740.33733210.31815988630996
1.9374-1.96510.30813540.29895905625997
1.9651-1.99440.3073470.28716171651899
1.9944-2.02560.2923390.26426056639599
2.0256-2.05880.26753510.26226200655199
2.0588-2.09430.28413430.25236078642199
2.0943-2.13240.26363080.23656229653799
2.1324-2.17340.27483390.224862126551100
2.1734-2.21770.22173020.212161266428100
2.2177-2.26590.27293430.208562356578100
2.2659-2.31860.23593120.196562256537100
2.3186-2.37660.22333180.190861236441100
2.3766-2.44090.23523550.178861866541100
2.4409-2.51270.22313340.182661876521100
2.5127-2.59370.20753080.174562506558100
2.5937-2.68640.21683620.166661706532100
2.6864-2.79390.19373260.16562096535100
2.7939-2.9210.20932930.169562296522100
2.921-3.0750.2143160.171662256541100
3.075-3.26750.17983320.165162866618100
3.2675-3.51960.20393160.156461496465100
3.5196-3.87340.17263120.144762476559100
3.8734-4.4330.16413370.13346192652999
4.433-5.58170.15013360.13816151648799
5.5817-35.90210.18422860.17595716600291
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)
10.6489-1.46930.29463.5246-0.25140.29440.30490.1466-0.386-0.7668-0.13630.56250.3395-0.0262-0.11110.63380.0118-0.17750.3908-0.0220.5618-15.8629-39.76566.2879
21.9482-0.0268-0.50582.0123-0.23492.57250.0529-0.12760.1205-0.16380.00620.3553-0.18050.0316-0.02110.1517-0.0332-0.06250.37350.01570.322-23.8177-5.468914.8066
30.1882-0.0395-0.20653.07650.50780.32580.25340.0024-0.3895-0.323-0.00820.44840.469-0.0046-0.0830.66960.0482-0.24840.3071-0.00830.4949-12.9933-48.17687.6269
40.37550.186-0.1130.32340.19270.33760.00820.4639-0.7158-0.75960.09880.36950.71880.11340.1811.28260.0479-0.43090.4215-0.18070.9484-4.2889-85.31029.2084
56.5303-1.0592-1.35341.55922.42877.7260.1734-0.327-0.59690.7976-0.13680.70470.2288-0.3698-0.02260.63710.0418-0.20850.39480.03860.7138-9.2143-68.435520.3294
62.2302-1.63240.77271.1823-0.55650.2540.49650.1129-0.0704-0.15850.01580.34220.89230.0888-0.49331.2745-0.1385-0.13550.56590.06480.7233-11.4484-42.758218.3261
70.202-0.17350.17786.59660.49760.22820.18050.0971-0.2792-0.110.0536-0.31630.39730.08950.04650.6540.0503-0.13570.2692-0.03990.51510.9979-55.787315.3419
80.30760.1762-0.20170.1206-0.110.14490.4359-0.1778-0.7840.3345-0.1970.15960.5883-0.08390.63211.8094-0.1561-0.68140.1971-0.07731.4947-1.9978-99.958217.6951
92.3934-2.2992-2.14172.27182.29222.99630.290.2873-0.46490.1568-0.1882-0.82640.38510.1405-0.08340.67040.28310.03120.4947-0.07041.036726.8081-69.705817.4945
10-0.13660.30360.06981.34790.2850.1453-0.01420.082-0.2681-0.4878-0.0196-0.990.13670.2411-0.03990.37560.07760.21610.39590.02030.691423.3942-28.375210.5462
112.711-0.8158-0.23745.80311.93280.9169-0.0482-0.0556-0.150.09740.0347-0.73120.16630.23360.05820.3244-0.03570.08160.36050.05510.352417.3866-11.853812.9094
121.2769-0.04960.1431.24780.45052.133-0.14610.20740.1014-0.538-0.0133-0.318-0.1350.16380.11830.2474-0.05450.09540.34420.03340.283313.05812.06126.3485
131.60850.35731.0573.31970.7983.8954-0.130.15940.1565-0.4113-0.0983-0.0973-0.1776-0.13040.19080.1859-0.06830.06310.30260.01860.22095.78633.2667.4066
145.5964.59863.17314.79752.76415.1502-0.0413-0.35750.3538-0.0522-0.38130.6583-0.0605-0.82440.31330.1593-0.02750.00970.4186-0.02310.2383-2.65713.924910.6718
151.3490.44810.5421.8269-0.21261.8384-0.04620.0844-0.0414-0.2011-0.109-0.1320.1662-0.06440.1480.1919-0.06340.08770.31460.00130.247.9622-3.155510.3933
160.99240.4370.41441.11910.28211.5982-0.17280.2595-0.2585-0.50840.0114-1.39650.17090.4040.18340.360.05580.18750.37250.00640.949323.0155-33.649610.0109
173.01-3.09421.01873.4485-0.56141.1273-0.078-0.0287-0.1554-0.21870.0095-0.61050.29960.40250.09960.50540.12450.04620.38180.00330.725921.5342-53.391217.5121
182.8334-0.962-0.2630.69140.84051.68060.14590.2594-0.6757-0.4701-0.0994-1.06440.73280.5939-0.52750.99090.41450.16970.496-0.07531.119227.9459-78.635212.4541
193.03133.07241.34946.9863-0.79623.0346-0.04480.0049-0.1215-0.86960.0990.9120.1010.0691-0.02810.89790.1810.03310.46850.00060.526414.6009-58.87766.6746
200.8897-0.22620.11281.50760.03430.80050.09720.1083-0.4943-0.41110.1119-0.49170.5330.28560.3440.72590.2219-0.01450.3276-0.11470.71615.9978-67.0314.8421
210.1875-1.3027-0.12784.63550.6924-0.6908-0.0926-0.0835-0.2570.72150.08470.14090.34430.09860.01340.71960.054-0.00910.35430.04830.3984-2.1747-37.529343.7091
222.23690.80990.41822.12110.11552.4327-0.0324-0.0250.25810.18190.00960.066-0.17990.1113-0.00070.1646-0.03580.00330.25710.01110.1377-2.1005-1.679239.7073
230.4764-0.64120.03051.43320.1635-0.0617-0.0367-0.0729-0.22960.88330.11610.18690.1160.1072-0.0680.72920.06970.02480.30830.06130.45910.1374-46.192441.6225
241.1849-0.1059-0.47891.2581-1.87758.85830.1538-0.0603-0.217-0.3120.13220.53090.1982-0.325-0.31540.59910.1019-0.16960.28990.02270.6113.6016-80.041132.3828
252.3091-2.63341.41696.5213-3.81722.8198-0.1863-0.2572-0.28560.50890.17590.28-0.062-0.3230.00690.60630.1163-0.09010.25370.03690.48112.7531-83.994644.1199
266.6586-2.09290.63347.1915-2.83017.82930.19110.41720.60460.2729-0.5766-1.5233-0.2350.33320.2980.56350.0086-0.1560.32110.00430.586415.5902-63.722235.3186
270.113-0.7258-0.72044.25854.22754.1834-0.74440.0268-0.52730.22260.35460.21940.05330.51370.38980.91020.17930.00230.74250.07550.8387.0464-38.860534.1556
280.513-1.85040.72914.2538-1.6011-0.14880.13490.0463-0.1666-0.1413-0.04510.17090.16270.0105-0.09210.55240.1124-0.04930.31670.03130.51732.6883-53.846126.9954
296.7156-2.42110.98944.67411.44371.95910.1886-0.028-0.3427-0.1930.00180.51920.3072-0.1228-0.25840.62690.0371-0.16420.32540.03540.636913.5618-95.249935.2053
304.0044-0.7591-0.53784.6433-0.33353.76060.1440.22130.1981-0.2174-0.03030.04160.17440.1731-0.13680.57280.105-0.14170.34880.02640.490423.0026-95.851235.5059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 11:104A11 - 104
2X-RAY DIFFRACTION2chain A and resid 105:269A105 - 269
3X-RAY DIFFRACTION3chain A and resid 270:324A270 - 324
4X-RAY DIFFRACTION4chain B and resid 1:37B1 - 37
5X-RAY DIFFRACTION5chain B and resid 38:57B38 - 57
6X-RAY DIFFRACTION6chain B and resid 58:67B58 - 67
7X-RAY DIFFRACTION7chain B and resid 68:132B68 - 132
8X-RAY DIFFRACTION8chain B and resid 133:170B133 - 170
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