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- PDB-4hfu: Crystal structure of Fab 8M2 in complex with a H2N2 influenza vir... -

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Basic information

Entry
Database: PDB / ID: 4hfu
TitleCrystal structure of Fab 8M2 in complex with a H2N2 influenza virus hemagglutinin
Components
  • Fab 8M2 heavy chain
  • Fab 8M2 light chain
  • Hemagglutinin HA1
  • Hemagglutinin HA2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.106 Å
AuthorsXu, R. / Wilson, I.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: A recurring motif for antibody recognition of the receptor-binding site of influenza hemagglutinin.
Authors: Xu, R. / Krause, J.C. / McBride, R. / Paulson, J.C. / Crowe, J.E. / Wilson, I.A.
History
DepositionOct 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
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
B: Hemagglutinin HA2
H: Fab 8M2 heavy chain
L: Fab 8M2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5755
Polymers104,1504
Non-polymers4241
Water00
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Fab 8M2 heavy chain
L: Fab 8M2 light chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Fab 8M2 heavy chain
L: Fab 8M2 light chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Fab 8M2 heavy chain
L: Fab 8M2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,72415
Polymers312,45112
Non-polymers1,2733
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area49620 Å2
ΔGint-268 kcal/mol
Surface area113210 Å2
MethodPISA
2
A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Fab 8M2 heavy chain
L: Fab 8M2 light chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)627,44930
Polymers624,90224
Non-polymers2,5466
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area104490 Å2
ΔGint-558 kcal/mol
Surface area221160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.590, 129.590, 536.885
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hemagglutinin HA1


Mass: 36573.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305+/1957(H2N2) / Gene: HA / Plasmid: pFastBac / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q67085, UniProt: P03451*PLUS
#2: Protein Hemagglutinin HA2


Mass: 20139.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305+/1957(H2N2) / Gene: HA / Plasmid: pFastBac / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q67085, UniProt: P03451*PLUS
#3: Antibody Fab 8M2 heavy chain


Mass: 23988.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEE6.4 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#4: Antibody Fab 8M2 light chain


Mass: 23448.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEE12.4 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#5: 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.: 1
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
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: 4.17 Å3/Da / Density % sol: 70.47 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% PEG6000, 0.1 M Na citrate, pH 4 and 1 M LiCl, vapor diffusion, sitting drop, temperature 293.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionRedundancy: 9.2 % / Av σ(I) over netI: 14.08 / Number: 277788 / Rmerge(I) obs: 0.118 / Χ2: 1.03 / D res high: 3.1 Å / D res low: 45 Å / Num. obs: 30241 / % possible obs: 94.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.674599.110.0541.0449.8
5.36.6710010.0841.05210.3
4.635.310010.0920.98610.4
4.214.6310010.1150.99910.4
3.914.2110010.1740.95510.4
3.683.9110010.2531.05310.1
3.493.6810010.3071.0969.2
3.343.4998.410.3581.0827.4
3.213.3485.110.3031.0666.1
3.13.216310.3151.0085.9
ReflectionResolution: 3.1→45 Å / Num. obs: 30241 / % possible obs: 94.6 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.118 / Χ2: 1.031 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.215.90.31519851.008163
3.21-3.346.10.30326711.066185.1
3.34-3.497.40.35831051.082198.4
3.49-3.689.20.30731751.0961100
3.68-3.9110.10.25331421.0531100
3.91-4.2110.40.17431710.9551100
4.21-4.6310.40.11531870.9991100
4.63-5.310.40.09232120.9861100
5.3-6.6710.30.08432371.0521100
6.67-459.80.05433561.044199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.71 Å41.9 Å
Translation2.71 Å41.9 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.8_1063refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.106→41.898 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8378 / SU ML: 0.28 / σ(F): 0 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 1373 5.03 %
Rwork0.1925 --
obs0.1953 27299 85.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 279.54 Å2 / Biso mean: 63.0562 Å2 / Biso min: 13.89 Å2
Refinement stepCycle: LAST / Resolution: 3.106→41.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7211 0 28 0 7239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037423
X-RAY DIFFRACTIONf_angle_d0.75310083
X-RAY DIFFRACTIONf_chiral_restr0.0531103
X-RAY DIFFRACTIONf_plane_restr0.0041300
X-RAY DIFFRACTIONf_dihedral_angle_d16.9982718
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1058-3.21680.247240.259136138512
3.2168-3.34560.3519790.25141326140545
3.3456-3.49770.34551410.26322882302396
3.4977-3.68210.28331610.228230013162100
3.6821-3.91260.25941620.205629943156100
3.9126-4.21440.23931400.179730363176100
4.2144-4.6380.20911620.151330273189100
4.638-5.3080.21991730.15230323205100
5.308-6.68320.22911650.18230763241100
6.6832-41.90220.23121660.18513191335799
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)
10.1627-0.0131-0.08890.3075-0.09690.2349-0.0657-0.04290.07960.09160.0088-0-0.46770.2268-0.21270.561-0.2437-0.11080.2839-0.12550.33259.710417.4291114.0919
20.8615-0.20991.57140.52730.52944.6235-0.0077-0.27570.5013-0.1476-0.1613-0.137-0.55120.098-0.06420.3199-0.2282-0.01410.37850.13780.363818.50218.606168.8532
30.6159-0.11470.33111.24530.24751.3121-0.0123-0.0093-0.0359-0.2314-0.0637-0.1405-0.15150.40340.05150.2349-0.07570.03910.25790.10180.270416.42039.078553.4668
41.1332-0.0162-0.3490.70550.16012.16110.11660.00220.0941-0.018-0.114-0.0733-0.77040.4714-0.02830.259-0.1154-0.05830.22830.02710.262211.954415.664196.7699
50.1640.14230.541.87170.49291.7682-0.2124-0.05220.3170.0664-0.1760.0847-0.72230.23460.04220.4294-0.0207-0.04290.3447-0.03760.30199.0714.2691132.2673
60.49010.19241.26150.67060.86613.50050.06290.00920.00040.1385-0.0749-0.31360.14360.5922-0.30090.1855-0.0724-0.03980.4602-0.01460.29216.9219.1792126.1375
71.01680.2125-2.15980.0501-0.41694.7928-0.0910.06190.1716-0.0180.15830.18760.13290.21660.12150.1443-0.0189-0.02380.3031-0.06730.435812.63363.606191.4081
85.719-0.0358-3.17972.13251.60433.37770.0747-0.00950.41680.13020.0013-0.3001-0.40030.10190.13290.466-0.1459-0.01660.45080.16890.67481.69719.218272.2154
90.4438-0.08270.38250.39940.232.9026-0.0087-0.01280.05270.19380.00560.0293-0.13840.02940.05520.1745-0.0527-0.07290.25240.00690.16972.89626.3555115.5808
102.52671.19872.79760.9681.27463.1477-0.07180.18310.13180.1572-0.0155-0.2996-0.18010.2683-0.00890.4957-0.0715-0.00150.3962-0.07280.465811.973511.2152151.7967
111.61310.15280.07590.89970.42980.74430.0443-0.0715-0.1110.26850.0273-0.4055-0.03620.47980.00890.5501-0.0699-0.11150.6268-0.11050.358320.11496.7825146.0518
124.62211.881-0.90480.7899-0.60482.67470.1787-0.1933-0.12210.2378-0.019-0.18690.30840.3177-0.02930.5961-0.1766-0.17340.5692-0.06540.327810.05734.6616158.6109
130.30540.2224-0.23430.4177-0.2130.78690.1738-0.12370.17680.2377-0.08670.066-0.3560.0378-0.56510.6237-0.18680.11030.29970.11520.339719.940736.268223.2417
141.9318-0.4127-0.68983.7702-1.05461.20340.0274-0.04360.01650.1254-0.0770.0128-0.4008-0.1118-0.01050.5777-0.05550.09490.15620.05450.272811.175630.438329.7862
151.813-0.53070.95151.96830.10234.52060.2169-0.0592-0.0818-0.3279-0.1929-0.22660.18540.0953-0.04420.4096-0.19510.03090.25350.04290.257913.692620.264826.1818
160.637-0.1032-0.56290.6746-0.65321.44540.0857-0.0926-0.0450.2097-0.0552-0.1768-0.36370.30740.24940.6156-0.06590.0110.22550.08140.30814.112730.946227.7756
171.1819-0.7678-0.00532.2467-0.08871.1774-0.3358-0.06740.13350.46520.18220.3786-0.3534-0.1529-0.06130.55270.04720.04330.19370.08850.31165.882751.3642-0.612
181.4033-0.58690.66610.8681-0.4490.9384-0.13710.04780.2443-0.0613-0.0125-0.3275-0.33990.03130.04310.5326-0.1132-0.11920.27590.07560.38359.852158.397-5.2156
191.12680.60.59071.5295-0.43040.76850.3680.15330.0852-0.00870.11790.4345-0.3616-0.35040.02150.79230.19470.1180.62180.31310.5453-11.859936.948124.061
200.5373-0.03230.46320.4018-0.47931.54430.3069-0.08090.09220.01250.12260.317-0.3806-0.4991-0.11480.75650.21010.20490.35410.18980.3646-6.369936.136733.1281
211.0511-1.09780.63115.13580.35950.73540.43640.1230.43490.13850.10980.0892-0.6058-0.25750.10650.99280.21040.24740.52230.25050.5833-5.721842.850328.0438
221.7661-1.7966-0.40474.39760.58940.26270.47280.2185-0.0772-0.28770.11230.40920.074-0.35-0.13410.5732-0.0267-0.08680.41550.24720.4049-0.618325.368229.3627
230.0991-0.07840.08380.1158-0.01590.1209-0.064-0.0277-0.0810.0622-0.0204-0.05940.04450.0659-0.11290.75820.1660.31260.51670.34670.808-13.470448.984114.3092
243.8192-0.7992-0.88341.61260.03672.01380.17390.2290.4347-0.17710.1579-0.0127-0.5028-0.265-0.19320.2862-0.04450.08350.4624-0.04880.38162.884746.9337-10.8761
252.0733-0.3945-1.11280.4755-0.2351.0975-0.26550.2577-0.41480.48390.12110.74230.2657-0.48960.09950.4315-0.06140.1880.31670.16770.6854-5.274940.0805-0.9909
261.5153-0.7445-0.52481.71880.28060.4516-0.0967-0.05740.36520.19740.0560.0306-0.3095-0.18590.03790.89680.35630.16980.4890.14610.7969-6.044352.834412.2498
270.13030.15990.33850.89320.48090.8814-0.1810.5146-0.52120.2141-0.25530.4605-0.1197-0.66620.0750.2697-0.02480.03420.6002-0.08250.5808-1.592138.3521-10.4969
280.23040.16320.59380.91971.15072.1915-0.27740.2464-0.1390.3647-0.35670.59230.4569-0.63510.26930.7332-0.03360.15031.1925-0.06750.9036-13.200943.2344-6.7182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 9:55)A9 - 55
2X-RAY DIFFRACTION2chain 'A' and (resseq 56:99)A56 - 99
3X-RAY DIFFRACTION3chain 'A' and (resseq 100:269)A100 - 269
4X-RAY DIFFRACTION4chain 'A' and (resseq 270:324)A270 - 324
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:26)B1 - 26
6X-RAY DIFFRACTION6chain 'B' and (resseq 27:57)B27 - 57
7X-RAY DIFFRACTION7chain 'B' and (resseq 58:67)B58 - 67
8X-RAY DIFFRACTION8chain 'B' and (resseq 68:74)B68 - 74
9X-RAY DIFFRACTION9chain 'B' and (resseq 75:137)B75 - 137
10X-RAY DIFFRACTION10chain 'B' and (resseq 138:145)B138 - 145
11X-RAY DIFFRACTION11chain 'B' and (resseq 146:158)B146 - 158
12X-RAY DIFFRACTION12chain 'B' and (resseq 159:172)B159 - 172
13X-RAY DIFFRACTION13chain 'H' and (resseq 2:25)H2 - 25
14X-RAY DIFFRACTION14chain 'H' and (resseq 26:52)H26 - 52
15X-RAY DIFFRACTION15chain 'H' and (resseq 53:66)H53 - 66
16X-RAY DIFFRACTION16chain 'H' and (resseq 67:111)H67 - 111
17X-RAY DIFFRACTION17chain 'H' and (resseq 112:188)H112 - 188
18X-RAY DIFFRACTION18chain 'H' and (resseq 189:215)H189 - 215
19X-RAY DIFFRACTION19chain 'L' and (resseq 1:18)L1 - 18
20X-RAY DIFFRACTION20chain 'L' and (resseq 19:75)L19 - 75
21X-RAY DIFFRACTION21chain 'L' and (resseq 76:90)L76 - 90
22X-RAY DIFFRACTION22chain 'L' and (resseq 91:102)L91 - 102
23X-RAY DIFFRACTION23chain 'L' and (resseq 103:113)L103 - 113
24X-RAY DIFFRACTION24chain 'L' and (resseq 114:128)L114 - 128
25X-RAY DIFFRACTION25chain 'L' and (resseq 129:163)L129 - 163
26X-RAY DIFFRACTION26chain 'L' and (resseq 164:174)L164 - 174
27X-RAY DIFFRACTION27chain 'L' and (resseq 175:197)L175 - 197
28X-RAY DIFFRACTION28chain 'L' and (resseq 198:212)L198 - 212

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