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- PDB-5umn: Crystal structure of C05 VPGSGW mutant bound to H3 influenza hema... -

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Basic information

Entry
Database: PDB / ID: 5umn
TitleCrystal structure of C05 VPGSGW mutant bound to H3 influenza hemagglutinin, HA1 subunit
Components
  • Antibody C05 VPGSGW mutant, heavy chain
  • Antibody C05, light chain
  • Hemagglutinin
KeywordsIMMUNE SYSTEM / Influenza / Fab / Hemagglutinin
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 (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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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
CITRATE ANION / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsWu, N.C. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
CitationJournal: Nat Commun / Year: 2017
Title: In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity.
Authors: Nicholas C Wu / Geramie Grande / Hannah L Turner / Andrew B Ward / Jia Xie / Richard A Lerner / Ian A Wilson /
Abstract: The relatively recent discovery and characterization of human broadly neutralizing antibodies (bnAbs) against influenza virus provide valuable insights into antiviral and vaccine development. ...The relatively recent discovery and characterization of human broadly neutralizing antibodies (bnAbs) against influenza virus provide valuable insights into antiviral and vaccine development. However, the factors that influence the evolution of high-affinity bnAbs remain elusive. We therefore explore the functional sequence space of bnAb C05, which targets the receptor-binding site (RBS) of influenza haemagglutinin (HA) via a long CDR H3. We combine saturation mutagenesis with yeast display to enrich for C05 variants of CDR H3 that bind to H1 and H3 HAs. The C05 variants evolve up to 20-fold higher affinity but increase specificity to each HA subtype used in the selection. Structural analysis reveals that the fine specificity is strongly influenced by a highly conserved substitution that regulates receptor binding in different subtypes. Overall, this study suggests that subtle natural variations in the HA RBS between subtypes and species may differentially influence the evolution of high-affinity bnAbs.
History
DepositionJan 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Hemagglutinin
C: Antibody C05 VPGSGW mutant, heavy chain
D: Antibody C05, light chain
E: Antibody C05 VPGSGW mutant, heavy chain
F: Antibody C05, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,36417
Polymers160,1256
Non-polymers2,23911
Water20,0511113
1
A: Hemagglutinin
E: Antibody C05 VPGSGW mutant, heavy chain
F: Antibody C05, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7436
Polymers80,0623
Non-polymers6813
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-21 kcal/mol
Surface area31360 Å2
MethodPISA
2
B: Hemagglutinin
C: Antibody C05 VPGSGW mutant, heavy chain
D: Antibody C05, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,62111
Polymers80,0623
Non-polymers1,5588
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-37 kcal/mol
Surface area30520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.344, 88.344, 255.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Antibody , 2 types, 4 molecules CEDF

#2: Antibody Antibody C05 VPGSGW mutant, heavy chain


Mass: 26304.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Antibody Antibody C05, light chain


Mass: 23367.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Hemagglutinin /


Mass: 30391.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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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Non-polymers , 4 types, 1120 molecules

#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1113 / Source method: isolated from a natural source / Formula: H2O

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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: 3.11 Å3/Da / Density % sol: 60.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate pH 5.5 and 9% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→88.4 Å / Num. obs: 136341 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rpim(I) all: 0.066 / Rsym value: 0.155 / Net I/σ(I): 15.4
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 13627 / CC1/2: 0.722 / Rpim(I) all: 0.353 / Rsym value: 0.82 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4FP8

4fp8


Resolution: 1.97→88.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.696 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 6721 4.9 %RANDOM
Rwork0.18124 ---
obs0.18254 129540 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.97→88.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10771 0 147 1113 12031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911245
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210052
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.95915282
X-RAY DIFFRACTIONr_angle_other_deg0.966323473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05851421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66924.304460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.181151781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3441557
X-RAY DIFFRACTIONr_chiral_restr0.10.21700
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112496
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022233
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1151.7945681
X-RAY DIFFRACTIONr_mcbond_other1.1121.7945680
X-RAY DIFFRACTIONr_mcangle_it22.6777103
X-RAY DIFFRACTIONr_mcangle_other22.6777104
X-RAY DIFFRACTIONr_scbond_it1.2171.9855564
X-RAY DIFFRACTIONr_scbond_other1.1881.9845562
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.042.8888179
X-RAY DIFFRACTIONr_long_range_B_refined7.44922.38512329
X-RAY DIFFRACTIONr_long_range_B_other7.44922.39212330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.971→2.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 475 -
Rwork0.244 9516 -
obs--99.02 %
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)
11.4324-0.13420.17660.92080.03490.969-0.03720.0706-0.11640.02670.0126-0.08920.10650.08260.02450.12590.00930.01780.12490.00860.0779-0.370284.361341.446
22.14720.11170.5670.99430.1271.2509-0.04850.07280.1593-0.0807-0.04320.115-0.2656-0.07050.09170.1440.0084-0.02020.0877-0.01550.07827.0442111.715549.322
30.55050.1747-0.08681.41760.72980.8205-0.0509-0.0971-0.07670.07660.0457-0.0103-0.00020.00380.00520.0572-0.0043-0.00210.1585-0.0090.133729.055472.721714.7334
40.9483-0.1397-0.27741.32130.5190.9434-0.02790.0554-0.0772-0.01740.0417-0.0862-0.00390.057-0.01390.00510.00790.00790.1365-0.0350.105844.607569.60944.8252
50.04550.00640.05691.5603-0.43180.36270.0032-0.0665-0.01840.0706-0.0617-0.16570.04390.02280.05850.1063-0.0059-0.00020.16590.03050.13071.0788134.998617.7195
60.44510.31950.00921.2557-0.34240.44990.0097-0.0065-0.002-0.02570.01260.10320.0845-0.0226-0.02230.09620.00640.00690.129-0.00570.07-11.5451138.16483.9803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 311
2X-RAY DIFFRACTION2B51 - 307
3X-RAY DIFFRACTION3C2 - 214
4X-RAY DIFFRACTION4D1 - 213
5X-RAY DIFFRACTION5E2 - 214
6X-RAY DIFFRACTION6F1 - 213

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