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- PDB-4hf5: Crystal structure of Fab 8F8 in complex a H2N2 influenza virus he... -

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Basic information

Entry
Database: PDB / ID: 4hf5
TitleCrystal structure of Fab 8F8 in complex a H2N2 influenza virus hemagglutinin
Components
  • (Hemagglutinin ...) x 2
  • Fab 8F8 heavy chain
  • Fab 8F8 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / hemagglutinin / antibody / viral receptor binding / antigen binding / sialic acid / 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 / 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
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
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.004 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 4, 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: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 / 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_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 / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_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 HA1
B: Hemagglutinin HA2
H: Fab 8F8 heavy chain
L: Fab 8F8 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6446
Polymers104,4714
Non-polymers1,1732
Water0
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Fab 8F8 heavy chain
L: Fab 8F8 light chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Fab 8F8 heavy chain
L: Fab 8F8 light chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Fab 8F8 heavy chain
L: Fab 8F8 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,93118
Polymers313,41212
Non-polymers3,5196
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Unit cell
Length a, b, c (Å)136.615, 136.615, 142.134
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1


Mass: 36504.227 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: C7S226
#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: C7S226

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Antibody , 2 types, 2 molecules HL

#3: Antibody Fab 8F8 heavy chain


Mass: 25140.242 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 8F8 light chain


Mass: 22686.938 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)

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Sugars , 2 types, 2 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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

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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: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 295.7 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 11% PEG4000, 0.1 M Tris, pH 8.5 and 0.1 M MgCl2, vapor diffusion, sitting drop, temperature 295.7K

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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: Mar 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionRedundancy: 3.9 % / Av σ(I) over netI: 11.55 / Number: 114153 / Rmerge(I) obs: 0.097 / Χ2: 1.08 / D res high: 3 Å / D res low: 50 Å / Num. obs: 29412 / % possible obs: 94.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465099.710.0371.1223.9
5.136.4610010.0590.9884
4.485.1399.910.071.0454.1
4.074.4810010.0911.0744.1
3.784.0710010.1351.0244.1
3.563.7810010.211.0794.1
3.383.5699.510.3061.1614
3.233.3895.710.3850.9493.7
3.113.2386.710.5111.243.3
33.1164.810.5891.2683.2
ReflectionResolution: 3→50 Å / Num. obs: 29412 / % possible obs: 94.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.097 / Χ2: 1.081 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.113.20.58919881.268164.8
3.11-3.233.30.51126451.24186.7
3.23-3.383.70.38529480.949195.7
3.38-3.5640.30630401.161199.5
3.56-3.784.10.2130731.0791100
3.78-4.074.10.13530841.0241100
4.07-4.484.10.09130911.0741100
4.48-5.134.10.0731341.045199.9
5.13-6.4640.05931400.9881100
6.46-503.90.03732691.122199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.004→44.718 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7691 / SU ML: 0.35 / σ(F): 0 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2822 1395 5.12 %
Rwork0.229 --
obs0.2318 27264 87.78 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.141 Å2 / ksol: 0.286 e/Å3
Displacement parametersBiso max: 618.23 Å2 / Biso mean: 98.2333 Å2 / Biso min: 25.78 Å2
Baniso -1Baniso -2Baniso -3
1-6.5736 Å2-0 Å2-0 Å2
2--6.5736 Å20 Å2
3----13.1472 Å2
Refinement stepCycle: LAST / Resolution: 3.004→44.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6561 0 78 0 6639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086981
X-RAY DIFFRACTIONf_angle_d1.2299235
X-RAY DIFFRACTIONf_chiral_restr0.0761008
X-RAY DIFFRACTIONf_plane_restr0.0051185
X-RAY DIFFRACTIONf_dihedral_angle_d22.0772510
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 (%)
3.0044-3.11170.3948620.3681476153850
3.1117-3.23630.39971100.33972082219272
3.2363-3.38350.36781250.29842406253182
3.3835-3.56180.34491430.27952566270989
3.5618-3.78490.32211490.24982736288594
3.7849-4.0770.25171560.21572789294596
4.077-4.48690.23141690.18572851302097
4.4869-5.13530.25851800.18472902308298
5.1353-6.46690.2881460.2112963310999
6.4669-44.72270.26561550.22973098325399
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)
10.19390.06240.03390.09710.060.03440.003-0.48270.14450.490.062-0.15090.023-0.0065-0.07071.30810.0886-0.31170.9028-0.79850.153-70.1401-19.7607141.2154
20.44190.21820.33850.14310.1520.2432-0.265-0.0293-0.04190.25080.0426-0.1349-0.2396-0.14120.19870.84160.07050.06950.449-0.08370.5725-69.4563-17.6406114.8347
30.42520.49340.25871.12070.80190.6267-0.08550.0010.4437-0.24130.07370.2423-0.74270.17330.35410.6006-0.1907-0.1924-0.0632-0.0270.2578-62.9451-11.73881.0492
40.95480.34930.34050.42060.52090.8258-0.05290.24370.0911-0.28950.01670.0913-0.0440.3226-0.0020.5921-0.01570.00110.39470.03710.4471-62.7891-18.827164.9954
50.92010.09290.15960.10890.08810.3599-0.15020.0213-0.5534-0.21260.1444-0.01440.112-0.14730.00310.590.0587-0.04390.4144-0.08660.5284-62.8727-27.723362.8749
60.89520.5294-0.68240.6874-0.05820.87980.5009-0.2453-0.29120.0755-0.29020.1338-0.23310.2493-0.02720.57890.1317-0.08610.3513-0.05820.5013-57.6071-19.752875.2365
70.25560.0478-0.1880.3170.4561.00170.0531-0.16230.22130.4128-0.26780.0075-0.0330.23050.05950.7909-0.03160.01930.4414-0.0130.4759-67.6913-17.7418109.5313
80.2766-0.2065-0.11910.15550.12360.21330.1105-0.45660.43360.619-0.03960.0936-0.61740.1157-0.04141.0075-0.10210.03790.6764-0.0830.3933-62.6907-22.6536141.1704
90.06320.17020.02280.48080.20430.7654-0.04130.01340.04060.03870.0651-0.0444-0.05730.129-0.05780.6635-0.0636-0.05020.5488-0.28220.1641-58.3845-30.5245112.6256
100.2328-0.2407-0.26680.26110.32140.4730.00730.14120.10060.14180.1025-0.0922-0.0670.1588-0.07781.4542-0.3642-0.13651.59750.21681.3627-63.85-29.1814101.1402
110.94330.08640.02990.37630.37910.6542-0.1245-0.30390.1280.32480.1185-0.076-0.3786-0.0372-0.02160.88590.074-0.05390.368-0.0040.4448-68.6152-32.7412120.3514
121.1783-0.0711-0.47940.7193-0.6240.7916-0.0342-0.0448-0.0620.1919-0.04840.0360.23-0.0742-0.08251.5768-0.13940.10421.8519-0.57450.4866-68.481-26.086157.3964
131.0745-0.40190.14910.96320.64540.7721-0.4514-0.37940.21070.5061-0.52390.08580.3083-0.95110.61921.9673-0.4415-0.27131.4708-0.24421.0499-57.4739-22.3024162.9553
140.31770.17990.00240.10330.0013-0.00020.2364-0.0263-0.18810.18660.0329-0.07880.14130.03970.0021.19670.1155-0.32991.7911-0.08550.3788-53.1829-25.4948155.9824
150.0557-0.07720.11820.1477-0.22840.34410.20690.03020.02850.24530.1706-0.20510.03690.3601-0.14281.65660.0906-0.35631.94340.11330.7615-59.0004-31.2986169.2238
160.45590.2521-0.00710.8332-0.4720.61260.05330.05860.1057-0.13620.02740.0344-0.0349-0.1708-0.03960.4840.0274-0.15070.1179-0.00780.3939-82.53641.748744.4412
171.1177-0.6892-1.08870.45030.78921.5692-0.26450.20940.08410.0688-0.4765-0.2314-0.1063-0.2340.35941.2307-0.0979-0.07561.4950.07371.1004-103.511213.079127.6966
181.1437-0.63260.38720.3697-0.08831.02470.14410.3807-0.6078-0.52280.04530.65450.57130.0062-0.24350.9921-0.0472-0.34140.6810.03820.9594-90.6711-15.849735.7454
190.31550.39620.32910.58740.34420.40580.5316-0.0696-0.3535-0.11210.2191-0.52690.6167-0.2104-0.31851.1747-0.3763-0.19580.62320.02251.0211-92.6933-21.557341.7682
200.3586-0.61870.45661.89160.41212.9025-0.10410.3749-0.2089-0.50010.03740.4462-0.03020.4091-0.02680.9207-0.0119-0.30550.5941-0.13230.7163-80.4382-9.849335.7413
210.60890.3481-0.08320.51070.35450.50680.3716-0.1287-0.1123-0.26770.40150.59790.2614-0.5021-0.32250.7442-0.1835-0.39110.93310.16541.2912-98.8976-13.219833.3982
221.0165-0.53650.06890.4303-0.34351.140.5663-0.09060.11260.03810.28150.4320.1234-0.4106-0.45950.93070.2416-0.10551.70150.12331.3149-110.90524.947416.0791
230.32860.75090.27391.75320.60420.2384-0.27180.22810.34570.1202-0.26970.2251-0.1243-0.4310.34581.1453-0.4535-0.13922.09540.14721.3203-108.3225-8.394325.0271
240.12010.42390.00631.55060.31071.0707-0.2840.10130.3494-0.0614-0.28050.2965-0.166-0.3860.34271.13220.038-0.19621.5282-0.06341.2095-104.83090.068726.6543
252.6074-0.15710.37413.3392-0.21432.3987-0.0169-0.1831-0.3778-0.37670.5120.4042-0.22370.0923-0.33231.4957-0.3976-0.15441.47750.11561.576-108.33390.81323.5099
260.54630.2216-0.39610.2585-0.15921.33350.2920.0531-0.25720.5657-0.13970.12631.6866-0.5919-0.12812.9762-0.8347-0.20542.14590.19221.1456-102.28776.41223.5538
270.5255-0.08250.06812.9625-2.08791.4731-0.25950.90170.0499-0.00020.0046-0.1197-0.7951-0.59590.27132.1543-0.0256-0.26542.05830.1811.0611-107.0748-6.121613.2754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 9:28)A9 - 28
2X-RAY DIFFRACTION2chain 'A' and (resseq 29:55)A29 - 55
3X-RAY DIFFRACTION3chain 'A' and (resseq 56:89)A56 - 89
4X-RAY DIFFRACTION4chain 'A' and (resseq 90:195)A90 - 195
5X-RAY DIFFRACTION5chain 'A' and (resseq 196:247)A196 - 247
6X-RAY DIFFRACTION6chain 'A' and (resseq 248:269)A248 - 269
7X-RAY DIFFRACTION7chain 'A' and (resseq 270:326)A270 - 326
8X-RAY DIFFRACTION8chain 'B' and (resseq 1:56)B1 - 56
9X-RAY DIFFRACTION9chain 'B' and (resseq 57:61)B57 - 61
10X-RAY DIFFRACTION10chain 'B' and (resseq 62:66)B62 - 66
11X-RAY DIFFRACTION11chain 'B' and (resseq 67:132)B67 - 132
12X-RAY DIFFRACTION12chain 'B' and (resseq 133:140)B133 - 140
13X-RAY DIFFRACTION13chain 'B' and (resseq 141:147)B141 - 147
14X-RAY DIFFRACTION14chain 'B' and (resseq 148:158)B148 - 158
15X-RAY DIFFRACTION15chain 'B' and (resseq 159:172)B159 - 172
16X-RAY DIFFRACTION16chain 'H' and (resseq 1:116)H1 - 116
17X-RAY DIFFRACTION17chain 'H' and (resseq 141:178)H141 - 178
18X-RAY DIFFRACTION18chain 'L' and (resseq 3:48)L3 - 48
19X-RAY DIFFRACTION19chain 'L' and (resseq 49:84)L49 - 84
20X-RAY DIFFRACTION20chain 'L' and (resseq 85:95)L85 - 95
21X-RAY DIFFRACTION21chain 'L' and (resseq 96:109)L96 - 109
22X-RAY DIFFRACTION22chain 'L' and (resseq 110:136)L110 - 136
23X-RAY DIFFRACTION23chain 'L' and (resseq 137:146)L137 - 146
24X-RAY DIFFRACTION24chain 'L' and (resseq 158:167)L158 - 167
25X-RAY DIFFRACTION25chain 'L' and (resseq 168:181)L168 - 181
26X-RAY DIFFRACTION26chain 'L' and (resseq 182:191)L182 - 191
27X-RAY DIFFRACTION27chain 'L' and (resseq 192:208)L192 - 208

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