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- PDB-4yk4: Human antibody 641 I-9 in complex with influenza hemagglutinin H1... -

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Basic information

Entry
Database: PDB / ID: 4yk4
TitleHuman antibody 641 I-9 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
Components
  • 641 I-9 VHCH antibody
  • 641 I-9 VLCL antibody
  • Hemagglutinin
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 / 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 (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 speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsSchmidt, A.G. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI089618 United States
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 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: 641 I-9 VLCL antibody
Z: 641 I-9 VHCH antibody
E: Hemagglutinin
B: 641 I-9 VLCL antibody
C: 641 I-9 VHCH antibody
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,14812
Polymers149,8216
Non-polymers1,3276
Water2,234124
1
Y: 641 I-9 VLCL antibody
Z: 641 I-9 VHCH antibody
E: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5746
Polymers74,9103
Non-polymers6643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 641 I-9 VLCL antibody
C: 641 I-9 VHCH antibody
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5746
Polymers74,9103
Non-polymers6643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)235.365, 130.154, 68.972
Angle α, β, γ (deg.)90.000, 105.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 641 I-9 VLCL antibody


Mass: 23353.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals)
#2: Antibody 641 I-9 VHCH antibody


Mass: 25587.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals)
#3: Protein Hemagglutinin /


Mass: 25968.922 Da / Num. of mol.: 2 / Fragment: UNP residues 65-280
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: unidentified baculovirus / References: UniProt: A7UPX0
#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.: 6
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 6% PEG 2000, 0.3M magnesium nitrate, 0.05M lithium sulfate, 2% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2013
Diffraction measurementDetails: 1.00 degrees, 1.0 sec, detector distance 350.00 mm / Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionAv R equivalents: 0.106 / Number: 146198
ReflectionResolution: 2.8→50 Å / Num. obs: 48068 / % possible obs: 96.1 % / Redundancy: 3 % / Biso Wilson estimate: 57.13 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.07 / Rrim(I) all: 0.128 / Χ2: 3.359 / Net I/av σ(I): 20.82 / Net I/σ(I): 11.9 / Num. measured all: 146198
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.853.10.58924240.6830.3950.7121.95699.5
2.85-2.93.10.49524980.7130.330.5982.10999.2
2.9-2.963.10.41924580.8060.2780.5052.27599.4
2.96-3.023.10.38324560.8240.2510.462.37898.9
3.02-3.083.10.31224690.890.2060.3752.60898.9
3.08-3.153.10.26824860.9230.1760.3222.72498.7
3.15-3.233.10.23524330.9330.1550.2822.89798.1
3.23-3.323.10.20324260.9480.1330.2443.22297.7
3.32-3.423.10.17724320.9670.1180.2143.38397.1
3.42-3.533.10.15624160.9690.1030.1883.69196.4
3.53-3.653.10.14124230.9720.0930.173.89396.3
3.65-3.83.10.12723670.9770.0840.1533.98595.7
3.8-3.9730.11323720.980.0750.1364.23194.5
3.97-4.1830.09323420.9870.0630.1134.19794.5
4.18-4.442.90.08123480.9860.0550.0994.3293.4
4.44-4.792.90.07323430.9890.050.0894.49392.9
4.79-5.272.80.06922850.9880.0470.0844.27892.2
5.27-6.032.90.07223650.990.0480.0864.18493.5
6.03-7.593.10.06623890.9910.0420.0783.6894.1
7.59-503.10.04923360.9950.0310.0583.49290.9
Cell measurementReflection used: 146198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HKX, 1HEZ, 1D5B

4hkx

1hez

1d5b


Resolution: 2.8→35.04 Å / FOM work R set: 0.7881 / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 1968 4.17 %
Rwork0.2203 45179 -
obs0.2219 47147 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.47 Å2 / Biso mean: 63.43 Å2 / Biso min: 27.62 Å2
Refinement stepCycle: final / Resolution: 2.8→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9919 0 84 124 10127
Biso mean--148.33 50.47 -
Num. residues----1277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210273
X-RAY DIFFRACTIONf_angle_d1.05913973
X-RAY DIFFRACTIONf_chiral_restr0.0661555
X-RAY DIFFRACTIONf_plane_restr0.0161777
X-RAY DIFFRACTIONf_dihedral_angle_d12.9113701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-2.87010.34651450.31943220336596
2.8701-2.94760.34811390.29493317345699
2.9476-3.03430.31161400.2923290343099
3.0343-3.13220.31341440.27853358350299
3.1322-3.24410.31821440.2623275341998
3.2441-3.37380.31551440.26983248339298
3.3738-3.52730.30211430.24173228337196
3.5273-3.7130.24431380.2323235337396
3.713-3.94540.25441420.21513194333695
3.9454-4.24950.26121420.20643170331294
4.2495-4.67630.19621360.17533146328293
4.6763-5.35090.20631290.1733152328193
5.3509-6.73370.2161460.19613172331894
6.7337-35.04250.26431360.2043174331092
Refinement TLS params.Method: refined / Origin x: -61.225 Å / Origin y: 8.3831 Å / Origin z: 8.1242 Å
111213212223313233
T0.0952 Å2-0.234 Å2-0.0089 Å2-0.1045 Å2-0.0516 Å2--0.128 Å2
L0.0279 °20.0212 °20.0795 °2-0.1178 °20.0988 °2--0.1274 °2
S-0.0144 Å °-0.0606 Å °0.0427 Å °-0.0434 Å °-0.1447 Å °0.0253 Å °-0.0377 Å °-0.0433 Å °-0.1125 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allY1 - 211
2X-RAY DIFFRACTION1allZ1 - 225
3X-RAY DIFFRACTION1allE55 - 260
4X-RAY DIFFRACTION1allB1 - 211
5X-RAY DIFFRACTION1allC1 - 225
6X-RAY DIFFRACTION1allA55 - 260
7X-RAY DIFFRACTION1allS1 - 126
8X-RAY DIFFRACTION1allD269 - 274

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