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- PDB-8g2k: Structure of the H3 hemagglutinin of A/California/7/2004 -

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Basic information

Entry
Database: PDB / ID: 8g2k
TitleStructure of the H3 hemagglutinin of A/California/7/2004
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / Hemagglutinin / antigen / homotrimer / native
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
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesAlphainfluenzavirus influenzae
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVenkatramani, L. / Mooers, B.H.M. / Air, G.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)NIH 2P20GM103640 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM145423 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 CA225520 United States
CitationJournal: To Be Published
Title: Structure of the H3 hemagglutinin of A/California/7/2004
Authors: Venkatramani, L. / Mooers, B.H.M. / Air, G.M.
History
DepositionFeb 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024-
Revision 2.0Oct 2, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_audit_support / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_contact_author / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / software / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_audit_support.country / _pdbx_branch_scheme.auth_mon_id / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_entity_branch_descriptor.descriptor / _pdbx_entity_branch_link.comp_id_1 / _pdbx_entity_branch_link.comp_id_2 / _pdbx_entity_branch_list.comp_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Chirality error
Details: NDGs are replaced by NAGS with the correct chrilaity
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 16, 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)57,85210
Polymers55,1082
Non-polymers2,7458
Water2,162120
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)173,55730
Polymers165,3236
Non-polymers8,23424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area43110 Å2
ΔGint-14 kcal/mol
Surface area60340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.199, 101.199, 384.462
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 35256.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Alphainfluenzavirus influenzae / Strain: A/California/7/2004 / References: UniProt: A4GXY4
#2: Protein Hemagglutinin


Mass: 19851.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Alphainfluenzavirus influenzae / Strain: A/California/7/2004 / References: UniProt: A3DRV6

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Sugars , 3 types, 8 molecules

#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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 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.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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, 120 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 310.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Pentaerythritol propoxylate (5/4 PO/OH), 200 mM KCl and 50 mM HEPES (pH 7.5 adjusted with KOH).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→34.25 Å / Num. obs: 31998 / % possible obs: 99.55 % / Observed criterion σ(F): 6 / Redundancy: 9.8 % / Biso Wilson estimate: 48.26 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.023 / Rrim(I) all: 0.073 / Rsym value: 0.066 / Net I/av σ(I): 22.4 / Net I/σ(I): 19.94
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 9617 / Rpim(I) all: 0.794 / Rrim(I) all: 0.348 / Rsym value: 0.83 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(dev_3973: ???)refinement
MOSFLM1.0.7data reduction
SCALA2.1data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→34.25 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 1638 5.12 %
Rwork0.2093 --
obs0.2106 31992 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 179 120 4169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034137
X-RAY DIFFRACTIONf_angle_d0.6085602
X-RAY DIFFRACTIONf_dihedral_angle_d12.1261551
X-RAY DIFFRACTIONf_chiral_restr0.047647
X-RAY DIFFRACTIONf_plane_restr0.003718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.420.32231330.28022361X-RAY DIFFRACTION95
2.42-2.50.28541280.27142498X-RAY DIFFRACTION100
2.5-2.590.28321290.25442519X-RAY DIFFRACTION100
2.59-2.690.28281380.25142488X-RAY DIFFRACTION100
2.69-2.810.25771250.27492534X-RAY DIFFRACTION100
2.81-2.960.27781390.2572520X-RAY DIFFRACTION100
2.96-3.150.27261300.23482532X-RAY DIFFRACTION100
3.15-3.390.25431410.23042520X-RAY DIFFRACTION100
3.39-3.730.25791560.21072529X-RAY DIFFRACTION100
3.73-4.270.20591520.17612547X-RAY DIFFRACTION100
4.27-5.370.17181390.15912582X-RAY DIFFRACTION100
5.38-34.250.22821280.20152724X-RAY DIFFRACTION100
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)
11.39040.25541.54731.72832.53614.1667-0.02450.02560.2033-0.20220.03830.0726-0.5209-0.56290.06610.40110.05760.07860.27720.02680.5529-5.18317.38106.42
22.0818-0.6508-0.12751.5427-0.21733.90370.30350.72610.5-0.5789-0.0402-0.0912-0.51820.0075-0.23730.7506-0.01280.14620.67230.1680.60556.14525.09956.758
31.35291.7019-0.74271.9877-0.7284.24820.19840.75270.314-0.50180.1113-0.22690.20930.9341-0.23510.8260.07130.26331.11330.10060.589116.32917.77641.767
42.2383-0.54820.11222.4219-0.97573.1361-0.01580.82660.1582-0.67780.1577-0.0773-0.3476-0.1727-0.18911.00880.00910.19311.12120.02990.503111.0213.60434.4
51.82650.5258-0.2231.73490.14985.24360.00210.54390.0332-0.52930.2014-0.1633-0.04920.5365-0.21750.7205-0.03490.16750.67660.09970.560911.63317.85851.074
61.66530.0667-2.39147.608-4.59247.32640.35960.1790.21640.13250.14170.0554-0.84340.1374-0.37920.4832-0.04230.15020.34460.03730.47022.36721.33174.999
71.4022-0.157-0.63141.2269-0.2652.4183-0.03680.20020.2729-0.00460.0562-0.012-0.4074-0.8256-0.12750.35050.07540.04360.30750.03350.5033-4.70315.792.562
84.8882-4.3614-3.20924.49441.12847.5710.80010.6382-1.51290.1902-0.7004-0.241-0.1096-0.3867-0.0980.38450.00240.00940.4187-0.03290.643-6.0617.921113.743
97.393-2.2217-3.67394.65420.34043.1065-0.0619-0.2439-0.4960.4149-0.07570.0781-0.7657-0.3042-0.00390.44650.02470.03150.351-0.07240.4868-2.3621.274113.942
105.9706-0.0141-1.16695.23183.68729.263-0.6108-1.03610.18740.5045-0.32140.5051-0.55460.08970.92520.55160.0308-0.00110.2807-0.08880.45830.34423128.405
111.9859-1.0823-2.14011.56892.414.81870.0060.00330.20590.1610.0020.1737-0.26891.34680.00090.3733-0.08950.060.2122-0.07120.57067.01816.574107.403
122.8451-1.9559-0.98942.78340.68330.35910.1726-0.07720.16690.053-0.49310.15420.87160.57550.14550.7152-0.23280.12690.53220.02220.68219.64513.30375.592
130.84870.11441.19040.80691.20347.3189-0.00110.17840.1363-0.10930.04140.0259-0.38580.1319-0.00870.334-0.00330.03580.28220.03230.4744-1.7327.3388.276
142.84820.14121.30975.2182-0.79815.97720.1626-0.26730.16720.315-0.1423-0.19340.0220.0433-0.05540.4175-0.0258-0.00280.3529-0.11510.46844.21512.567134.33
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:41 )A8 - 41
2X-RAY DIFFRACTION2( CHAIN A AND ( RESID 42:104 OR RESID 401:401 ) )A42 - 104
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 42:104 OR RESID 401:401 ) )A401
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 105:135 OR RESID 402:402 OR RESID 403:403 ) )A105 - 135
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 105:135 OR RESID 402:402 OR RESID 403:403 ) )A402
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 105:135 OR RESID 402:402 OR RESID 403:403 ) )A403
7X-RAY DIFFRACTION4( CHAIN A AND RESID 136:246 )A136 - 246
8X-RAY DIFFRACTION5( CHAIN A AND RESID 247:274 )A247 - 274
9X-RAY DIFFRACTION6( CHAIN A AND RESID 275:304 )A275 - 304
10X-RAY DIFFRACTION7( CHAIN A AND RESID 305:325 )A305 - 325
11X-RAY DIFFRACTION8( CHAIN B AND RESID 1:10 )B1 - 10
12X-RAY DIFFRACTION9( CHAIN B AND RESID 11:22 )B11 - 22
13X-RAY DIFFRACTION10( CHAIN B AND RESID 23:30 )B23 - 30
14X-RAY DIFFRACTION11( CHAIN B AND RESID 31:55 )B31 - 55
15X-RAY DIFFRACTION12( CHAIN B AND RESID 56:65 )B56 - 65
16X-RAY DIFFRACTION13( CHAIN B AND RESID 66:126 )B66 - 126
17X-RAY DIFFRACTION14( CHAIN B AND ( RESID 127:173 OR RESID 201:201 ) )B127 - 173
18X-RAY DIFFRACTION14( CHAIN B AND ( RESID 127:173 OR RESID 201:201 ) )B201

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