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- PDB-5cjs: Crystal structure of a monomeric influenza hemagglutinin stem in ... -

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Entry
Database: PDB / ID: 5cjs
TitleCrystal structure of a monomeric influenza hemagglutinin stem in complex with an broadly neutralizing antibody CR9114
Components
  • CR9114 heavy chain
  • CR9114 light chain
  • Designed influenza hemagglutinin stem #4454, HA1
  • Designed influenza hemagglutinin stem #4454, HA2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / hemagglutinin / trimer / influenza / immunogen / monoclonal / antibody / neutralizing / influenza vaccine / glycoprotein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: Science / Year: 2015
Title: A stable trimeric influenza hemagglutinin stem as a broadly protective immunogen.
Authors: Impagliazzo, A. / Milder, F. / Kuipers, H. / Wagner, M.V. / Zhu, X. / Hoffman, R.M. / van Meersbergen, R. / Huizingh, J. / Wanningen, P. / Verspuij, J. / de Man, M. / Ding, Z. / Apetri, A. / ...Authors: Impagliazzo, A. / Milder, F. / Kuipers, H. / Wagner, M.V. / Zhu, X. / Hoffman, R.M. / van Meersbergen, R. / Huizingh, J. / Wanningen, P. / Verspuij, J. / de Man, M. / Ding, Z. / Apetri, A. / Kukrer, B. / Sneekes-Vriese, E. / Tomkiewicz, D. / Laursen, N.S. / Lee, P.S. / Zakrzewska, A. / Dekking, L. / Tolboom, J. / Tettero, L. / van Meerten, S. / Yu, W. / Koudstaal, W. / Goudsmit, J. / Ward, A.B. / Meijberg, W. / Wilson, I.A. / Radosevic, K.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: CR9114 light chain
H: CR9114 heavy chain
C: Designed influenza hemagglutinin stem #4454, HA1
D: Designed influenza hemagglutinin stem #4454, HA2
E: CR9114 light chain
F: CR9114 heavy chain
J: Designed influenza hemagglutinin stem #4454, HA1
K: Designed influenza hemagglutinin stem #4454, HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,11211
Polymers151,4488
Non-polymers6643
Water00
1
L: CR9114 light chain
H: CR9114 heavy chain
C: Designed influenza hemagglutinin stem #4454, HA1
D: Designed influenza hemagglutinin stem #4454, HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9455
Polymers75,7244
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-59 kcal/mol
Surface area29420 Å2
MethodPISA
2
E: CR9114 light chain
F: CR9114 heavy chain
J: Designed influenza hemagglutinin stem #4454, HA1
K: Designed influenza hemagglutinin stem #4454, HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1666
Polymers75,7244
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-57 kcal/mol
Surface area30830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.869, 110.869, 359.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody CR9114 light chain


Mass: 22712.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody CR9114 heavy chain


Mass: 24423.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper)
#3: Protein Designed influenza hemagglutinin stem #4454, HA1


Mass: 6673.505 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#4: Protein Designed influenza hemagglutinin stem #4454, HA2


Mass: 21915.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.21 Å3/Da / Density % sol: 70.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, pH 8.0, 0.2 M disodium hydrogen phosphate, 22% w/v PEG4000

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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: Apr 29, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / Num. obs: 18316 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rsym value: 0.21 / Net I/σ(I): 9.1
Reflection shellResolution: 4.3→4.37 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.92 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.3→48.01 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.303 929 5.09 %
Rwork0.262 --
obs0.264 18248 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.3→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9534 0 42 0 9576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099782
X-RAY DIFFRACTIONf_angle_d1.86513293
X-RAY DIFFRACTIONf_dihedral_angle_d15.6553489
X-RAY DIFFRACTIONf_chiral_restr0.221489
X-RAY DIFFRACTIONf_plane_restr0.0081716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3-4.51530.37871420.32712333X-RAY DIFFRACTION97
4.5153-4.7980.35131300.31612460X-RAY DIFFRACTION100
4.798-5.1680.28541370.29112398X-RAY DIFFRACTION100
5.168-5.68730.30571350.28182459X-RAY DIFFRACTION100
5.6873-6.50860.3581440.28372479X-RAY DIFFRACTION100
6.5086-8.19350.2821150.25812523X-RAY DIFFRACTION100
8.1935-48.01070.26621260.21812667X-RAY DIFFRACTION100

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