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- PDB-5jw3: Structure of MEDI8852 Fab Fragment in Complex with H7 HA -

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Basic information

Entry
Database: PDB / ID: 5jw3
TitleStructure of MEDI8852 Fab Fragment in Complex with H7 HA
Components
  • (Hemagglutinin) x 2
  • MEDI8852 heavy chain
  • MEDI8852 light chain
KeywordsIMMUNE SYSTEM / Antibody Influenza Broadly Neutralizing
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 speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.75 Å
AuthorsCollins, P.J. / Neu, U. / Walker, P.A. / Vorlaender, M.K. / Ogrodowicz, R.W. / Martin, S.R. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Cell / Year: 2016
Title: Structure and Function Analysis of an Antibody Recognizing All Influenza A Subtypes.
Authors: Kallewaard, N.L. / Corti, D. / Collins, P.J. / Neu, U. / McAuliffe, J.M. / Benjamin, E. / Wachter-Rosati, L. / Palmer-Hill, F.J. / Yuan, A.Q. / Walker, P.A. / Vorlaender, M.K. / Bianchi, S. ...Authors: Kallewaard, N.L. / Corti, D. / Collins, P.J. / Neu, U. / McAuliffe, J.M. / Benjamin, E. / Wachter-Rosati, L. / Palmer-Hill, F.J. / Yuan, A.Q. / Walker, P.A. / Vorlaender, M.K. / Bianchi, S. / Guarino, B. / De Marco, A. / Vanzetta, F. / Agatic, G. / Foglierini, M. / Pinna, D. / Fernandez-Rodriguez, B. / Fruehwirth, A. / Silacci, C. / Ogrodowicz, R.W. / Martin, S.R. / Sallusto, F. / Suzich, J.A. / Lanzavecchia, A. / Zhu, Q. / Gamblin, S.J. / Skehel, J.J.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_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_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
H: MEDI8852 heavy chain
L: MEDI8852 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,5297
Polymers101,1344
Non-polymers1,3943
Water00
1
A: Hemagglutinin
B: Hemagglutinin
H: MEDI8852 heavy chain
L: MEDI8852 light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: MEDI8852 heavy chain
L: MEDI8852 light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: MEDI8852 heavy chain
L: MEDI8852 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,58621
Polymers303,40312
Non-polymers4,1839
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area52620 Å2
ΔGint-188 kcal/mol
Surface area111020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.990, 143.990, 130.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 34533.840 Da / Num. of mol.: 1 / Fragment: UNP residues 19-334 / Source method: isolated from a natural source
Source: (natural) Influenza A virus (A/turkey/Italy/214845/2002(H7N3))
References: UniProt: Q701U0, UniProt: Q6GYW3*PLUS
#2: Protein Hemagglutinin


Mass: 19679.570 Da / Num. of mol.: 1 / Fragment: UNP residues 340-509 / Source method: isolated from a natural source
Source: (natural) Influenza A virus (A/turkey/Italy/214845/2002(H7N3))
References: UniProt: Q701U0, UniProt: Q6GYW3*PLUS

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Antibody , 2 types, 2 molecules HL

#3: Antibody MEDI8852 heavy chain


Mass: 24470.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Antibody MEDI8852 light chain


Mass: 22450.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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Sugars , 3 types, 3 molecules

#5: 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
#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
#7: 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.: 1
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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Details

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: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 45% PEP 15/4, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.75→48.433 Å / Num. obs: 15424 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 3.56 % / Biso Wilson estimate: 136.98 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.89
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.75-3.851.2711.1195.3
3.85-3.950.9181.48195.3
3.95-4.070.6482.06194
4.07-4.190.4942.67193.2
4.19-4.330.3793.78195.3
4.33-4.480.2784.67194.8
4.48-4.650.235.73194.4
4.65-4.840.216.2193.9
4.84-5.060.1926.44193
5.06-5.30.1697.81193.2
5.3-5.590.1628.12194.1
5.59-5.930.1369.32193.9
5.93-6.340.11510.96193
6.34-6.850.09912.23191.5
6.85-7.50.07117.78192.4
7.5-8.390.04624.07192.6
8.39-9.680.0333.29191.8
9.68-11.860.02144.9189.7
11.86-16.770.0245.87190.4
16.770.01852.09182.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BSG (chains A+B) and 5JW5 (chains H+L)

4bsg

5jw5


Resolution: 3.75→48.433 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.35
RfactorNum. reflection% reflection
Rfree0.2631 1210 7.85 %
Rwork0.2242 --
obs0.2269 15416 93.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 289.49 Å2 / Biso mean: 151.4283 Å2 / Biso min: 100.5 Å2
Refinement stepCycle: final / Resolution: 3.75→48.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7051 0 92 0 7143
Biso mean--128.64 --
Num. residues----914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077299
X-RAY DIFFRACTIONf_angle_d1.2319880
X-RAY DIFFRACTIONf_chiral_restr0.0681102
X-RAY DIFFRACTIONf_plane_restr0.0051280
X-RAY DIFFRACTIONf_dihedral_angle_d14.62657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.7501-3.90020.32281430.32441581172495
3.9002-4.07770.30531270.30091548167594
4.0777-4.29250.28471470.2621554170194
4.2925-4.56130.3171220.22791595171795
4.5613-4.91310.23581260.21681585171194
4.9131-5.4070.24421570.23071550170793
5.407-6.1880.25681300.22631579170994
6.188-7.7910.22921560.22461558171492
7.791-48.43710.26541020.18251656175890
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)
10.5732-0.2133-0.35570.50140.54563.38980.24780.0438-0.2514-0.0194-0.0350.17210.6190.025401.42220.02320.05241.2449-0.04421.337467.804722.46120.7864
21.26080.4030.41512.3975-0.79512.0766-0.12940.67460.0463-1.78510.0150.532-0.1973-0.488202.08580.0383-0.30181.6147-0.0811.683657.730523.4839-33.2521
32.12271.7961-1.15671.6168-1.36642.3045-0.0921.20660.4364-2.4117-0.07080.01020.1203-0.214-03.71830.1819-0.57772.5640.15971.768957.279729.7678-52.0161
41.03250.1257-0.53391.1686-0.20724.35410.0826-0.1899-0.1350.2299-0.12360.15750.0218-0.2792-0.01751.370.0582-0.00091.30890.01851.281566.94230.275619.5456
53.35331.71390.5236.1517-1.69013.8120.0915-0.1952-0.53590.3934-0.20840.55940.3433-0.1401-01.4184-0.02060.1561.2984-0.03641.434453.68172.342427.9312
64.423-0.10640.18034.734-1.86340.7584-0.02020.19320.2651-0.42990.02231.4592-0.1323-0.4497-01.49430.0779-0.10231.4423-0.12661.850140.134616.665615.9354
73.4127-0.92851.87593.3712-1.34491.23110.67020.7539-0.5814-0.3246-0.30170.6990.81140.9438-01.8070.1712-0.14631.8749-0.18812.624329.5237-16.216117.2681
81.28060.31041.94261.39831.2213.56510.2091-0.47190.56980.317-0.09991.89380.4153-0.2133-01.48560.02580.03641.8695-0.14953.357614.4967-9.377918.8191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 1:46 or resseq 260:316)A1 - 46
2X-RAY DIFFRACTION1chain A and (resseq 1:46 or resseq 260:316)A260 - 316
3X-RAY DIFFRACTION2chain A and (resseq 47:108 or resseq 251:259)A47 - 108
4X-RAY DIFFRACTION2chain A and (resseq 47:108 or resseq 251:259)A251 - 259
5X-RAY DIFFRACTION3chain A and (resseq 109:250)A109 - 250
6X-RAY DIFFRACTION4chain BB1 - 170
7X-RAY DIFFRACTION5chain H and resseq 1:130H1 - 130
8X-RAY DIFFRACTION6chain L and resseq 4:103L4 - 103
9X-RAY DIFFRACTION7chain H and resseq 131:229H131 - 229
10X-RAY DIFFRACTION8chain L and resseq 104:210L104 - 210

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