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- PDB-4mc5: Crystal structure of a subtype H18 hemagglutinin homologue from A... -

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Basic information

Entry
Database: PDB / ID: 4mc5
TitleCrystal structure of a subtype H18 hemagglutinin homologue from A/flat-faced bat/Peru/033/2010 (H18N11)
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / bat / influenza
Function / homologyHemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Alpha-Beta Complex / Alpha Beta / alpha-L-fucopyranose
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.238 Å
AuthorsYang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Stevens, J.
CitationJournal: Plos Pathog. / Year: 2013
Title: New world bats harbor diverse influenza a viruses.
Authors: Tong, S. / Zhu, X. / Li, Y. / Shi, M. / Zhang, J. / Bourgeois, M. / Yang, H. / Chen, X. / Recuenco, S. / Gomez, J. / Chen, L.M. / Johnson, A. / Tao, Y. / Dreyfus, C. / Yu, W. / McBride, R. / ...Authors: Tong, S. / Zhu, X. / Li, Y. / Shi, M. / Zhang, J. / Bourgeois, M. / Yang, H. / Chen, X. / Recuenco, S. / Gomez, J. / Chen, L.M. / Johnson, A. / Tao, Y. / Dreyfus, C. / Yu, W. / McBride, R. / Carney, P.J. / Gilbert, A.T. / Chang, J. / Guo, Z. / Davis, C.T. / Paulson, J.C. / Stevens, J. / Rupprecht, C.E. / Holmes, E.C. / Wilson, I.A. / Donis, R.O.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / 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 / _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_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_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_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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,79521
Polymers172,3893
Non-polymers7,40718
Water17,421967
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21000 Å2
ΔGint103 kcal/mol
Surface area63400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)239.093, 239.093, 161.228
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-1004-

HOH

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Components

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Protein / Non-polymers , 2 types, 970 molecules ABC

#1: Protein Hemagglutinin


Mass: 57462.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/flat-faced bat/Peru/033/2010 (H18N11) / Production host: Trichoplusia ni (cabbage looper)
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 967 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 6 types, 18 molecules

#2: 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
#3: 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)-[alpha-L-fucopyranose-(1-3)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1203.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1b_1-5]/1-2-1-3-4-4-5/a3-b1_a4-c1_a6-g1_c4-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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-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
#5: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][beta-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1221m-1b_1-5]/1-2-1-3/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-FUC / alpha-L-fucopyranose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 0.05 M calcium chloride, 30% PEG550 MME, 0.1 M Bis-Tris, pH 6.5, under oil, MICROBATCH, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.238→50 Å / Num. all: 111074 / Num. obs: 111074 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.238→2.32 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.238→48.019 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 20.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 5561 5.01 %
Rwork0.175 --
all0.18 111074 -
obs0.1765 111073 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.238→48.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11766 0 486 967 13219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512559
X-RAY DIFFRACTIONf_angle_d0.96617073
X-RAY DIFFRACTIONf_dihedral_angle_d22.1144741
X-RAY DIFFRACTIONf_chiral_restr0.061964
X-RAY DIFFRACTIONf_plane_restr0.0042156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.238-2.26360.23281770.2253351X-RAY DIFFRACTION97
2.2636-2.29020.24741900.21163485X-RAY DIFFRACTION100
2.2902-2.31820.24691780.20243478X-RAY DIFFRACTION100
2.3182-2.34750.25721950.20173498X-RAY DIFFRACTION100
2.3475-2.37840.24271930.19983444X-RAY DIFFRACTION100
2.3784-2.4110.22581630.20173530X-RAY DIFFRACTION100
2.411-2.44540.26521880.19223468X-RAY DIFFRACTION100
2.4454-2.48190.23121560.1893505X-RAY DIFFRACTION100
2.4819-2.52070.25942040.19823499X-RAY DIFFRACTION100
2.5207-2.5620.25541710.19063501X-RAY DIFFRACTION100
2.562-2.60620.23681810.19383503X-RAY DIFFRACTION100
2.6062-2.65360.24931550.19153494X-RAY DIFFRACTION100
2.6536-2.70460.24851910.19683494X-RAY DIFFRACTION100
2.7046-2.75980.23331950.19333486X-RAY DIFFRACTION100
2.7598-2.81980.23161850.19253516X-RAY DIFFRACTION100
2.8198-2.88540.25411940.19283507X-RAY DIFFRACTION100
2.8854-2.95760.23871820.19633485X-RAY DIFFRACTION100
2.9576-3.03750.22061700.18833538X-RAY DIFFRACTION100
3.0375-3.12690.24521830.19473494X-RAY DIFFRACTION100
3.1269-3.22780.23291780.20133542X-RAY DIFFRACTION100
3.2278-3.34310.2221870.19173531X-RAY DIFFRACTION100
3.3431-3.4770.2042010.17853498X-RAY DIFFRACTION100
3.477-3.63520.19511890.16283524X-RAY DIFFRACTION100
3.6352-3.82670.16991990.15723541X-RAY DIFFRACTION100
3.8267-4.06640.16332010.14573521X-RAY DIFFRACTION100
4.0664-4.38010.15461890.13283539X-RAY DIFFRACTION100
4.3801-4.82060.15722020.12833563X-RAY DIFFRACTION100
4.8206-5.51720.171750.15113602X-RAY DIFFRACTION100
5.5172-6.94780.20471980.18063602X-RAY DIFFRACTION100
6.9478-48.02960.18071910.18823773X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 299.9628 Å / Origin y: 209.7686 Å / Origin z: 13.3659 Å
111213212223313233
T0.1953 Å2-0.0057 Å20.0034 Å2-0.2091 Å2-0.0339 Å2--0.2152 Å2
L0.2991 °2-0.1725 °2-0.1254 °2-0.1768 °20.0925 °2--0.2331 °2
S-0.0192 Å °-0.0141 Å °-0.035 Å °0.0063 Å °0.0226 Å °-0.0236 Å °-0.0145 Å °0.0557 Å °0 Å °
Refinement TLS groupSelection details: all

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