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- PDB-5w0d: Inferred precursor (UCA) of the human antibody lineage K03.12 in ... -

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Basic information

Entry
Database: PDB / ID: 5w0d
TitleInferred precursor (UCA) of the human antibody lineage K03.12 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
Components
  • (Lineage K03.12 UCA antibody ...) x 2
  • Hemagglutinin HA1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / influenza neutralizing antibody germline precursor / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


immunoglobulin complex / 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 ...immunoglobulin complex / 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 / plasma 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin / IGL@ protein / IgG H chain
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsMcCarthy, K.R. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI089618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U19AI117892-01 United States
CitationJournal: Immunity / Year: 2018
Title: Memory B Cells that Cross-React with Group 1 and Group 2 Influenza A Viruses Are Abundant in Adult Human Repertoires.
Authors: McCarthy, K.R. / Watanabe, A. / Kuraoka, M. / Do, K.T. / McGee, C.E. / Sempowski, G.D. / Kepler, T.B. / Schmidt, A.G. / Kelsoe, G. / Harrison, S.C.
History
DepositionMay 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / 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 / _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 2.1Oct 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 HA1
B: Lineage K03.12 UCA antibody heavy chain
C: Lineage K03.12 UCA antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0329
Polymers74,1153
Non-polymers1,9186
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint3 kcal/mol
Surface area29870 Å2
Unit cell
Length a, b, c (Å)40.620, 61.660, 83.860
Angle α, β, γ (deg.)106.57, 95.25, 106.70
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hemagglutinin HA1


Mass: 25140.014 Da / Num. of mol.: 1 / Fragment: UNP residues 73-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: D1MPH2, UniProt: A7UPX0*PLUS

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Antibody , 2 types, 2 molecules BC

#2: Antibody Lineage K03.12 UCA antibody heavy chain


Mass: 26570.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: S6B2A6
#3: Antibody Lineage K03.12 UCA antibody light chain


Mass: 22403.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q6IPQ0

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Sugars , 2 types, 3 molecules

#4: 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.: 2
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
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 249 molecules

#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 200 mM sodium chloride, 100 mM PIPES, pH 6.0, 20% w/v PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 26, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.899→50 Å / Num. obs: 54618 / % possible obs: 94.2 % / Redundancy: 4.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1121 / Net I/σ(I): 8.22
Reflection shellResolution: 1.899→1.967 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.395 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 5534 / CC1/2: 0.536 / % possible all: 93.86

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5W0D & 5UGY

5w0d

5ugy


Resolution: 1.899→39.85 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 2715 4.98 %
Rwork0.196 --
obs0.198 54497 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 125 246 5350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085249
X-RAY DIFFRACTIONf_angle_d1.0337160
X-RAY DIFFRACTIONf_dihedral_angle_d22.2861906
X-RAY DIFFRACTIONf_chiral_restr0.059793
X-RAY DIFFRACTIONf_plane_restr0.006901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.93360.4121170.42162781X-RAY DIFFRACTION92
1.9336-1.97070.37591350.32612722X-RAY DIFFRACTION95
1.9707-2.0110.33011530.28672730X-RAY DIFFRACTION94
2.011-2.05470.33391270.26562757X-RAY DIFFRACTION95
2.0547-2.10250.31151260.27872735X-RAY DIFFRACTION94
2.1025-2.15510.30331330.26392735X-RAY DIFFRACTION94
2.1551-2.21330.32011250.26292690X-RAY DIFFRACTION93
2.2133-2.27850.40731510.27542762X-RAY DIFFRACTION95
2.2785-2.3520.31661440.24482711X-RAY DIFFRACTION94
2.352-2.4360.27921360.23242781X-RAY DIFFRACTION96
2.436-2.53360.25741500.22142753X-RAY DIFFRACTION94
2.5336-2.64880.27021540.21882568X-RAY DIFFRACTION91
2.6488-2.78850.28741720.21542733X-RAY DIFFRACTION95
2.7885-2.96310.22941420.20772769X-RAY DIFFRACTION95
2.9631-3.19180.22411430.19442747X-RAY DIFFRACTION95
3.1918-3.51280.23371610.17472588X-RAY DIFFRACTION91
3.5128-4.02070.20191540.15762793X-RAY DIFFRACTION96
4.0207-5.06410.14211610.13642685X-RAY DIFFRACTION93
5.0641-39.8590.20171310.16562742X-RAY DIFFRACTION95
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)
13.7579-1.28861.41828.2256-2.2032.36160.2933-0.3276-0.44280.7703-0.3075-0.30690.19710.36110.02320.3797-0.0371-0.07580.32340.09320.355611.16592.426-28.5201
22.33021.20190.14225.8328-1.01621.52690.06120.09370.036-0.2461-0.05650.07110.0725-0.0131-0.00170.20260.01850.04020.2078-0.01250.26851.64338.6659-43.0151
32.21230.46160.21823.76580.14571.68270.0954-0.16890.05380.5849-0.07760.6577-0.0095-0.1938-0.0020.2373-0.02740.09770.24160.01230.3884-4.310912.5084-34.1921
43.56191.8114-0.65266.2786-1.31884.5760.1975-0.35050.7450.1261-0.09920.0369-0.4650.1763-0.18580.31120.0340.05390.20460.03930.500711.224452.0636-53.1523
51.3379-0.0685-0.31522.6389-0.29941.88060.13680.08810.2937-0.146-0.0706-0.3231-0.20240.0847-0.03090.1966-0.00890.04670.21580.06450.460614.036241.8162-54.1087
60.2151.0652-0.91593.7001-3.35293.64580.03840.04470.0641-0.0607-0.1421-0.0982-0.1350.1390.1210.23820.02880.04850.24570.04320.42178.965242.8561-57.204
72.5248-0.3169-1.47164.71120.310.96720.0730.8028-0.1803-0.3090.22680.2751-0.1880.1789-0.33730.6576-0.0747-0.1430.52980.1110.4828.104369.4533-89.5907
83.01351.66260.89023.0724-0.83234.1649-0.0288-0.0749-0.02090.62670.40030.3192-0.6614-0.6589-0.29160.77140.0926-0.01480.41850.06450.387.442973.0478-80.2625
93.3951-0.31143.25762.6726-0.66234.4801-0.38510.2110.67550.48940.12680.0512-1.65470.12540.25141.1092-0.01090.03610.43490.12040.58913.470979.2331-85.3386
104.50841.07071.08894.45-1.06914.41540.1410.70580.0316-0.36-0.10680.0180.0614-0.0108-0.04320.24810.08190.03270.32620.00420.2765-3.180935.9865-69.1296
115.27961.9302-1.29524.0044-1.12794.2797-0.24140.2502-0.1255-0.23110.4716-0.13810.2438-0.1757-0.23470.5285-0.0513-0.06290.39140.00360.24479.917657.6485-87.8747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 174 )
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 263 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 17 )
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 91 )
6X-RAY DIFFRACTION6chain 'B' and (resid 92 through 144 )
7X-RAY DIFFRACTION7chain 'B' and (resid 145 through 165 )
8X-RAY DIFFRACTION8chain 'B' and (resid 166 through 223 )
9X-RAY DIFFRACTION9chain 'B' and (resid 224 through 235 )
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 107 )
11X-RAY DIFFRACTION11chain 'C' and (resid 108 through 211 )

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