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- PDB-3fku: Crystal structure of influenza hemagglutinin (H5) in complex with... -

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Basic information

Entry
Database: PDB / ID: 3fku
TitleCrystal structure of influenza hemagglutinin (H5) in complex with a broadly neutralizing antibody F10
Components
  • (Hemagglutinin) x 2
  • Neutralizing antibody F10
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / influenza / hemagglutinin / neutralizing antibody / scFv / H5 / F10 / Cell membrane / Envelope protein / Fusion protein / Membrane / Transmembrane / Virion / Cleavage on pair of basic residues / Glycoprotein / Lipoprotein / Palmitate / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


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 / membrane / identical protein binding
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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHwang, W.C. / Santelli, E. / Stec, B. / Wei, G. / Cadwell, G. / Bankston, L.A. / Sui, J. / Perez, S. / Aird, D. / Chen, L.M. ...Hwang, W.C. / Santelli, E. / Stec, B. / Wei, G. / Cadwell, G. / Bankston, L.A. / Sui, J. / Perez, S. / Aird, D. / Chen, L.M. / Ali, M. / Murakami, A. / Yammanuru, A. / Han, T. / Cox, N. / Donis, R.O. / Liddington, R.C. / Marasco, W.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses.
Authors: Sui, J. / Hwang, W.C. / Perez, S. / Wei, G. / Aird, D. / Chen, L.M. / Santelli, E. / Stec, B. / Cadwell, G. / Ali, M. / Wan, H. / Murakami, A. / Yammanuru, A. / Han, T. / Cox, N.J. / ...Authors: Sui, J. / Hwang, W.C. / Perez, S. / Wei, G. / Aird, D. / Chen, L.M. / Santelli, E. / Stec, B. / Cadwell, G. / Ali, M. / Wan, H. / Murakami, A. / Yammanuru, A. / Han, T. / Cox, N.J. / Bankston, L.A. / Donis, R.O. / Liddington, R.C. / Marasco, W.A.
History
DepositionDec 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
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
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
X: Neutralizing antibody F10
Y: Neutralizing antibody F10
Z: Neutralizing antibody F10
S: Neutralizing antibody F10
T: Neutralizing antibody F10
U: Neutralizing antibody F10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)538,42830
Polymers532,36218
Non-polymers6,06612
Water0
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
X: Neutralizing antibody F10
Y: Neutralizing antibody F10
Z: Neutralizing antibody F10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,21415
Polymers266,1819
Non-polymers3,0336
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36400 Å2
ΔGint-145 kcal/mol
Surface area92700 Å2
2
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
S: Neutralizing antibody F10
T: Neutralizing antibody F10
U: Neutralizing antibody F10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,21415
Polymers266,1819
Non-polymers3,0336
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31770 Å2
ΔGint-127 kcal/mol
Surface area95840 Å2
Unit cell
Length a, b, c (Å)205.300, 118.500, 338.900
Angle α, β, γ (deg.)90.00, 99.60, 90.00
Int Tables number5
Space group name H-MC121
DetailsTwo biological assemblies are present in the asymmetric unit. Chains A, B, C, D, E, F, X, Y, Z constitute one assembly. Chains G, H, I, J, K, L, S, T, U constitute the other assembly.

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Components

#1: Protein
Hemagglutinin / / Hemagglutinin HA1 chain


Mass: 38466.625 Da / Num. of mol.: 6 / Fragment: HA1
Source method: isolated from a genetically manipulated source
Details: Influenza A virus (A/Viet Nam/1203/2004(H5N1)) / Source: (gene. exp.) Influenza A virus / Strain: H5N1Influenza A virus subtype H5N1 / Gene: HA / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q6DQ33, UniProt: Q6J8F6*PLUS
#2: Protein
Hemagglutinin / / Hemagglutinin HA2 chain


Mass: 20980.234 Da / Num. of mol.: 6 / Fragment: HA2
Source method: isolated from a genetically manipulated source
Details: Influenza A virus (A/Viet Nam/1203/2004(H5N1)) / Source: (gene. exp.) Influenza A virus / Strain: H5N1Influenza A virus subtype H5N1 / Gene: HA / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q2F4V2, UniProt: Q6J8F6*PLUS
#3: Antibody
Neutralizing antibody F10


Mass: 29280.178 Da / Num. of mol.: 6 / Fragment: Single chain antibody
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSyn I / Production host: Escherichia coli (E. coli)
#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.: 6
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
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.: 6
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
Sequence detailsHA (CHAINS A B C D E F G H I J K L) RESIDUE NUMBERS IN THE PRIMARY CITATION DIFFER FROM THE ...HA (CHAINS A B C D E F G H I J K L) RESIDUE NUMBERS IN THE PRIMARY CITATION DIFFER FROM THE NUMBERING IN THIS ENTRY AND FOLLOW THAT IN PDB ENTRY 2FK0

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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: 3.82 Å3/Da / Density % sol: 67.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12.5% PEG 1K, 25% ethylene glycol, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 21, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. all: 132456 / Num. obs: 112570 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 4.5 % / Rmerge(I) obs: 0.128
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.95 / % possible all: 68.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.856 / SU B: 54.186 / SU ML: 0.409 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28623 5676 5 %RANDOM
Rwork0.23186 ---
obs0.23461 106885 85.01 %-
all-132456 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.629 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.14 Å2
2---0.21 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34573 0 402 0 34975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02235823
X-RAY DIFFRACTIONr_bond_other_d0.0010.0224140
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.95348613
X-RAY DIFFRACTIONr_angle_other_deg0.9013.00458667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64154383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39124.8151701
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.373155942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.55315183
X-RAY DIFFRACTIONr_chiral_restr0.0750.25306
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0239828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027023
X-RAY DIFFRACTIONr_nbd_refined0.210.28102
X-RAY DIFFRACTIONr_nbd_other0.1960.225480
X-RAY DIFFRACTIONr_nbtor_refined0.1850.216992
X-RAY DIFFRACTIONr_nbtor_other0.0910.220210
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2804
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.030.26
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.465228089
X-RAY DIFFRACTIONr_mcbond_other0.36728969
X-RAY DIFFRACTIONr_mcangle_it3.353335238
X-RAY DIFFRACTIONr_scbond_it4.507416365
X-RAY DIFFRACTIONr_scangle_it6.731613375
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 346 -
Rwork0.317 6225 -
obs--68.37 %
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)
10.4170.0547-0.68530.5916-0.66074.7115-0.0230.2580.175-0.3901-0.04390.0845-0.2881-0.3740.0669-0.0952-0.0277-0.0757-0.27420.0869-0.24828.6807-24.1326-73.9895
20.63250.34030.46741.02481.647910.56370.02830.02740.07120.0835-0.03750.0337-0.06950.00850.0092-0.54580.088-0.0328-0.5393-0.038-0.437330.8224-32.7922-19.4521
30.7740.0892-0.00520.44051.12624.8296-0.07540.3977-0.0732-0.2861-0.0036-0.1924-0.13340.54120.079-0.14870.09140.1321-0.27620.0399-0.24754.0374-49.3112-73.9528
40.4996-0.13950.83410.7145-0.68059.7861-0.08090.00540.00240.12350.0247-0.01210.15050.02490.0561-0.5028-0.0232-0.0356-0.50310.0748-0.432945.586-46.6971-19.4757
50.42110.00781.09010.4316-0.38394.3746-0.06260.2545-0.1362-0.2943-0.03090.13050.425-0.10620.0934-0.2352-0.0567-0.0009-0.1008-0.1268-0.225519.4741-58.6273-73.9596
60.7926-0.0265-1.09710.63910.11118.1892-0.0381-0.0647-0.10250.0126-0.0840.0292-0.0956-0.2240.1222-0.4623-0.01840.0445-0.5206-0.0003-0.39826.1761-52.496-19.4207
70.7460.1237-0.18851.1488-0.99733.17450.0489-0.0316-0.0937-0.05630.06120.09720.2112-0.4557-0.11-0.253-0.04130.0692-0.28280.0567-0.107251.1973.203-98.5565
81.21520.77011.80231.51021.867513.3861-0.05330.5831-0.1302-0.58950.2730.01950.44020.4626-0.21970.11370.08580.04750.0655-0.008-0.021258.66777.1539-151.4976
90.7106-0.06480.82990.82750.66913.7363-0.00830.0063-0.1581-0.0641-0.0013-0.27570.27650.35890.0096-0.3190.03320.0388-0.0818-0.0704-0.008687.14286.5301-98.5204
101.80350.129-2.27120.82010.39649.55030.01930.6178-0.0638-0.52560.1436-0.21370.00890.2084-0.16290.0950.05630.19030.0796-0.10780.066179.873510.8217-151.4003
110.7994-0.0302-0.88560.86470.12284.57850.07650.02970.2564-0.0480.035-0.2046-0.35150.0382-0.1115-0.14180.06950.0923-0.3093-0.0556-0.105966.380835.9407-98.5436
120.6571-0.48090.23661.8286-3.217212.03660.05720.3910.1552-0.64270.0386-0.0430.0622-0.5208-0.09580.1084-0.06530.14660.09180.0541-0.018466.128327.4716-151.493
131.42730.47590.65521.78230.13110.7265-0.08550.3017-0.01520.1089-0.0264-0.1344-0.01930.07450.1119-0.00490.0290.1180.0536-0.0305-0.0043108.562717.559-146.2323
143.2212-0.55320.73931.64660.23820.25560.1586-0.06370.032-0.1745-0.21390.15630.0287-0.00720.05530.07720.06090.1009-0.03870.08050.000745.878349.0562-146.0646
150.5411-0.8634-0.30413.37390.23320.4844-0.15650.0002-0.1347-0.4030.144-0.0651-0.11220.01030.01250.0743-0.13050.0329-0.0007-0.06260.001350.0482-20.9434-145.9264
162.0039-0.6302-0.4590.9928-0.0450.5395-0.05880.0021-0.1841-0.09610.05790.0047-0.0357-0.17120.0009-0.0004-0.0610.03360.0686-0.04170.0269-3.7101-60.655-26.2533
172.0830.80480.40431.42140.44720.1557-0.01950.01060.1643-0.109-0.01690.1803-0.12020.10160.03640.1446-0.0008-0.0664-0.0349-0.0001-0.019738.5938-2.8655-26.2977
180.5687-0.4779-0.01652.3151-0.30110.2532-0.01790.08060.0204-0.0571-0.0521-0.22120.12240.0630.070.01620.0560.00930.07750.03950.005767.6477-68.4718-26.3428
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 326
2X-RAY DIFFRACTION2B1 - 180
3X-RAY DIFFRACTION3C4 - 326
4X-RAY DIFFRACTION4D1 - 180
5X-RAY DIFFRACTION5E4 - 326
6X-RAY DIFFRACTION6F1 - 180
7X-RAY DIFFRACTION7G4 - 326
8X-RAY DIFFRACTION8H1 - 172
9X-RAY DIFFRACTION9I4 - 326
10X-RAY DIFFRACTION10J1 - 172
11X-RAY DIFFRACTION11K4 - 326
12X-RAY DIFFRACTION12L1 - 172
13X-RAY DIFFRACTION13S1 - 249
14X-RAY DIFFRACTION14T1 - 249
15X-RAY DIFFRACTION15U1 - 249
16X-RAY DIFFRACTION16X1 - 249
17X-RAY DIFFRACTION17Y1 - 249
18X-RAY DIFFRACTION18Z1 - 249

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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