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- PDB-5k9j: Crystal structure of multidonor HV6-1-class broadly neutralizing ... -

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Basic information

Entry
Database: PDB / ID: 5k9j
TitleCrystal structure of multidonor HV6-1-class broadly neutralizing Influenza A antibody 56.a.09 isolated following H5 immunization.
Components
  • 56.a.09 heavy chain
  • 56.a.09 light chain
KeywordsIMMUNE SYSTEM / Influenza / multidonor / H5 / universal influenza vaccine
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å
AuthorsJoyce, M.G. / Thomas, P.V. / Wheatley, A.K. / McDermott, A.B. / Mascola, J.R. / Kwong, P.D.
CitationJournal: Cell / Year: 2016
Title: Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses.
Authors: Joyce, M.G. / Wheatley, A.K. / Thomas, P.V. / Chuang, G.Y. / Soto, C. / Bailer, R.T. / Druz, A. / Georgiev, I.S. / Gillespie, R.A. / Kanekiyo, M. / Kong, W.P. / Leung, K. / Narpala, S.N. / ...Authors: Joyce, M.G. / Wheatley, A.K. / Thomas, P.V. / Chuang, G.Y. / Soto, C. / Bailer, R.T. / Druz, A. / Georgiev, I.S. / Gillespie, R.A. / Kanekiyo, M. / Kong, W.P. / Leung, K. / Narpala, S.N. / Prabhakaran, M.S. / Yang, E.S. / Zhang, B. / Zhang, Y. / Asokan, M. / Boyington, J.C. / Bylund, T. / Darko, S. / Lees, C.R. / Ransier, A. / Shen, C.H. / Wang, L. / Whittle, J.R. / Wu, X. / Yassine, H.M. / Santos, C. / Matsuoka, Y. / Tsybovsky, Y. / Baxa, U. / Mullikin, J.C. / Subbarao, K. / Douek, D.C. / Graham, B.S. / Koup, R.A. / Ledgerwood, J.E. / Roederer, M. / Shapiro, L. / Kwong, P.D. / Mascola, J.R. / McDermott, A.B.
History
DepositionMay 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 56.a.09 heavy chain
L: 56.a.09 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7154
Polymers47,6552
Non-polymers3,0602
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-23 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.790, 103.758, 59.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody 56.a.09 heavy chain


Mass: 24465.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 56.a.09 light chain


Mass: 23189.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M sodium acetate, pH 5.5, 25% (w/v) PEG-400 and 11% (w/v) PEG-8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25791 / % possible obs: 99 % / Redundancy: 6.8 % / Net I/σ(I): 18.29

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bvk, 4lss

1bvk

4lss


Resolution: 1.904→35.124 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 1249 4.84 %
Rwork0.1952 --
obs0.197 25791 65.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.904→35.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 24 143 3519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043454
X-RAY DIFFRACTIONf_angle_d0.774695
X-RAY DIFFRACTIONf_dihedral_angle_d11.4022078
X-RAY DIFFRACTIONf_chiral_restr0.049534
X-RAY DIFFRACTIONf_plane_restr0.005593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9038-1.980.459370.342147X-RAY DIFFRACTION4
1.98-2.07010.4049280.2545549X-RAY DIFFRACTION13
2.0701-2.17920.2939600.2281392X-RAY DIFFRACTION34
2.1792-2.31570.28921420.23812387X-RAY DIFFRACTION58
2.3157-2.49450.23371670.23863283X-RAY DIFFRACTION80
2.4945-2.74540.26831870.23984073X-RAY DIFFRACTION98
2.7454-3.14240.29172070.21714159X-RAY DIFFRACTION100
3.1424-3.95830.20942110.18544207X-RAY DIFFRACTION100
3.9583-35.130.20342400.16824345X-RAY DIFFRACTION100
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)
12.5648-2.0436-2.21962.79971.86422.379-0.20240.0759-0.3820.13230.2204-0.16670.29340.4251-0.03290.25940.04550.00050.3885-0.1410.499718.029736.1852-15.2912
21.9837-0.65410.23161.784-0.24481.83850.15140.34130.3104-0.69130.2408-1.0292-0.29510.70950.2490.0517-0.07580.1610.4192-0.28880.628820.544243.4542-20.8975
30.036-0.3449-0.18582.06251.08443.3730.0640.2599-0.0798-0.24580.1242-0.27040.02280.2804-0.16720.2375-0.03180.05570.3738-0.14990.471113.242940.3318-22.5334
41.437-0.7486-0.74851.3803-0.66451.47140.3519-0.1082-1.21690.2422-0.0426-0.00770.5333-0.31390.02820.3238-0.0767-0.0940.24580.07950.57-9.099129.9406-4.4489
50.85221.1474-0.16023.98850.10282.88860.0576-0.2127-1.11960.25060.0382-0.23190.598-0.0270.1240.3266-0.0186-0.03830.21420.07330.6979-8.878429.0469-4.6845
60.74260.66850.72714.570.89823.30790.6207-0.7597-0.28960.1876-0.2735-0.26570.7485-0.29120.14440.5239-0.0827-0.26050.64930.29160.6588-8.20624.13062.446
75.07291.2606-1.66881.6773-0.26192.75940.44050.14161.2879-0.2618-0.24760.2547-0.3875-0.0977-0.13150.39520.00840.03120.4052-0.00910.7407-1.167443.2439-38.2722
84.47620.12040.23721.39861.1364.00590.4738-0.1031-0.00150.07090.11320.04430.09470.0971-0.08920.2656-0.03030.02220.3478-0.12650.42436.47835.4486-32.1356
95.9864-0.2595-0.05161.7811-0.20563.54140.16060.1226-0.0277-0.144-0.05040.03150.02160.0422-0.19190.23850.0135-0.02790.3458-0.09930.38832.593634.1818-38.2826
103.07030.4249-1.7781.0895-0.5774.04170.0619-0.0983-0.4795-0.0405-0.0512-0.11450.0463-0.1053-0.31120.2432-0.0584-0.06110.2288-0.00560.3432-9.755636.0393-16.7439
113.22411.0984-1.15442.63941.68499.20470.31720.07490.4263-0.25320.36210.3929-0.2916-0.808-0.34590.266-0.0843-0.03120.30870.0710.3796-21.735636.8011-12.0124
123.62220.8906-0.58473.1580.7085.42330.3699-0.09810.38070.1250.10340.4334-0.2582-0.7442-0.24920.2711-0.0941-0.03060.44530.08020.4748-23.342837.1874-7.7154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 33 )
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 82 )
3X-RAY DIFFRACTION3chain 'H' and (resid 82A through 111 )
4X-RAY DIFFRACTION4chain 'H' and (resid 112 through 165 )
5X-RAY DIFFRACTION5chain 'H' and (resid 166 through 203 )
6X-RAY DIFFRACTION6chain 'H' and (resid 204 through 215 )
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 29 )
8X-RAY DIFFRACTION8chain 'L' and (resid 30 through 48 )
9X-RAY DIFFRACTION9chain 'L' and (resid 49 through 91 )
10X-RAY DIFFRACTION10chain 'L' and (resid 92 through 128 )
11X-RAY DIFFRACTION11chain 'L' and (resid 129 through 150 )
12X-RAY DIFFRACTION12chain 'L' and (resid 151 through 211 )

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