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- PDB-4yjz: Human antibody H2526 in complex with influenza hemagglutinin H1 S... -

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Basic information

Entry
Database: PDB / ID: 4yjz
TitleHuman antibody H2526 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
Components
  • Hemagglutinin
  • scFv H2526
KeywordsViral protein/Immune system / influenza / antibody / complex / hemagglutinin / 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 (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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...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 / 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: 2.72 Å
AuthorsSchmidt, A.G. / Harrison, S.C.
CitationJournal: Cell / Year: 2015
Title: Viral receptor-binding site antibodies with diverse germline origins.
Authors: Schmidt, A.G. / Therkelsen, M.D. / Stewart, S. / Kepler, T.B. / Liao, H.X. / Moody, M.A. / Haynes, B.F. / Harrison, S.C.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / pdbx_validate_chiral / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Hemagglutinin
L: scFv H2526
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7415
Polymers53,0782
Non-polymers6643
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint2 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.149, 153.166, 177.628
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Hemagglutinin


Mass: 25109.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7UPX0
#2: Antibody scFv H2526


Mass: 27967.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals)
#3: 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.: 3
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsChain L in this structure is a single-chain variable fragment (scFv) which includes the variable ...Chain L in this structure is a single-chain variable fragment (scFv) which includes the variable heavy and variable light domains of an antibody with a linker in-between (GGGGGGSGGGGSGGGGS). Authors intentionally chose to begin numbering of the variable heavy at 201 after the linker region.

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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: 4.05 Å3/Da / Density % sol: 69.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES, 30% PEG 400 and 0.1M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99998 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2014
Diffraction measurementDetails: 1.00 degrees, 5.0 sec, detector distance 350.01 mm / Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionAv R equivalents: 0.07 / Number: 135025
ReflectionResolution: 2.72→50 Å / Num. obs: 23649 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/av σ(I): 39.699
Reflection shellResolution: 2.72→2.77 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.892 / Rsym value: 0.648 / % possible all: 100
Cell measurementReflection used: 135025

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBN, 4HKX

3gbn

4hkx


Resolution: 2.72→39.703 Å / FOM work R set: 0.7241 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 1152 4.87 %
Rwork0.2295 22487 -
obs0.2312 23639 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182.19 Å2 / Biso mean: 90.78 Å2 / Biso min: 46.68 Å2
Refinement stepCycle: final / Resolution: 2.72→39.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 42 48 3556
Biso mean--131.07 83.27 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113607
X-RAY DIFFRACTIONf_angle_d1.4054905
X-RAY DIFFRACTIONf_chiral_restr0.052529
X-RAY DIFFRACTIONf_plane_restr0.019635
X-RAY DIFFRACTIONf_dihedral_angle_d15.551284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.72-2.84170.41651280.357827762904100
2.8417-2.99140.37141600.326127522912100
2.9914-3.17880.34761370.315428002937100
3.1788-3.42410.32331400.277127722912100
3.4241-3.76840.31121550.255627922947100
3.7684-4.31320.27211500.22428022952100
4.3132-5.43190.21991350.18942831296699
5.4319-39.70680.21321470.19682962310999

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