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- PDB-4jlr: Crystal structure of a designed Respiratory Syncytial Virus Immun... -

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Basic information

Entry
Database: PDB / ID: 4jlr
TitleCrystal structure of a designed Respiratory Syncytial Virus Immunogen in complex with Motavizumab
Components
  • Motavizumab Fab heavy chain
  • Motavizumab Fab light chain
  • RSV_1Isea designed scaffold
KeywordsIMMUNE SYSTEM / Antibody / designed immunogen / Specific Binding / RSV F protein
Function / homologyRibosome-recycling factor / Topoisomerase I; Chain A, domain 4 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsRupert, P.B. / Correia, B. / Schief, W. / Strong, R.K.
CitationJournal: Nature / Year: 2014
Title: Proof of principle for epitope-focused vaccine design.
Authors: Correia, B.E. / Bates, J.T. / Loomis, R.J. / Baneyx, G. / Carrico, C. / Jardine, J.G. / Rupert, P. / Correnti, C. / Kalyuzhniy, O. / Vittal, V. / Connell, M.J. / Stevens, E. / Schroeter, A. ...Authors: Correia, B.E. / Bates, J.T. / Loomis, R.J. / Baneyx, G. / Carrico, C. / Jardine, J.G. / Rupert, P. / Correnti, C. / Kalyuzhniy, O. / Vittal, V. / Connell, M.J. / Stevens, E. / Schroeter, A. / Chen, M. / Macpherson, S. / Serra, A.M. / Adachi, Y. / Holmes, M.A. / Li, Y. / Klevit, R.E. / Graham, B.S. / Wyatt, R.T. / Baker, D. / Strong, R.K. / Crowe, J.E. / Johnson, P.R. / Schief, W.R.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Apr 9, 2014Group: Source and taxonomy
Revision 1.4Dec 17, 2014Group: Data collection
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Motavizumab Fab heavy chain
L: Motavizumab Fab light chain
S: RSV_1Isea designed scaffold
A: Motavizumab Fab heavy chain
B: Motavizumab Fab light chain
C: RSV_1Isea designed scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7777
Polymers123,5396
Non-polymers2381
Water1,76598
1
H: Motavizumab Fab heavy chain
L: Motavizumab Fab light chain
S: RSV_1Isea designed scaffold


Theoretical massNumber of molelcules
Total (without water)61,7703
Polymers61,7703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Motavizumab Fab heavy chain
B: Motavizumab Fab light chain
C: RSV_1Isea designed scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0084
Polymers61,7703
Non-polymers2381
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.159, 158.511, 116.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Motavizumab Fab heavy chain


Mass: 24226.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#2: Antibody Motavizumab Fab light chain


Mass: 23092.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#3: Protein RSV_1Isea designed scaffold


Mass: 14450.532 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 20% PEG 1000, 0.1M lithium sulfate, 0.04M phosphate-citrate, 2% glycerol, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.111
SYNCHROTRONALS 5.0.121
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMay 31, 2012
ADSC QUANTUM 315r2CCDJul 19, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal, cylindrically bent, Si(220)SINGLE WAVELENGTHMx-ray1
2Single crystal, cylindrically bent, Si(220)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 37548 / Num. obs: 37515 / % possible obs: 99.91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.5
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 6.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→45.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 26.628 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24926 1867 5 %RANDOM
Rwork0.19134 ---
obs0.19424 35615 99.32 %-
all-37548 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.54 Å2
Baniso -1Baniso -2Baniso -3
1--3.95 Å20 Å20 Å2
2--2.04 Å20 Å2
3---1.92 Å2
Refine analyzeLuzzati coordinate error obs: 0.752 Å
Refinement stepCycle: LAST / Resolution: 2.71→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7806 0 12 98 7916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.028002
X-RAY DIFFRACTIONr_bond_other_d0.0010.027374
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.95310890
X-RAY DIFFRACTIONr_angle_other_deg0.7283.00216988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65551033
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54724.492305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.255151252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9961530
X-RAY DIFFRACTIONr_chiral_restr0.0670.21255
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021758
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 124 -
Rwork0.238 2465 -
obs--94.18 %
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)
14.83130.5750.13482.2652-1.55834.1968-0.37641.17210.1891-0.56360.1310.3265-0.12520.51310.24530.2381-0.1093-0.17460.69840.01840.144731.63150.927-4.684
25.43011.77530.31423.4126-0.71623.3783-0.3063-0.0780.63210.14510.0915-0.0762-0.51530.72110.21480.1072-0.041-0.08930.5414-0.08390.130553.8558.15319.699
315.2346-11.7152.005413.487-3.0070.78711.22521.4051.0328-0.2929-0.94470.561-0.23720.2961-0.28051.3014-0.1108-0.09691.3010.11810.62562.51966.731-17.976
43.0191-0.5795-0.53511.86081.22912.6859-0.0059-0.1083-0.01410.41760.0883-0.16770.1790.0673-0.08230.117-0.0186-0.06610.14920.06230.0616-18.17450.9276.032
51.7733-1.3199-1.66183.36171.70625.73850.03140.38450.1139-0.3836-0.14130.7058-0.5608-0.60490.10990.1416-0.0594-0.13290.30110.09460.2751-4465.365-10.769
611.96796.82420.187511.44672.93994.30330.5782-0.88160.49361.24530.1719-1.2762-0.20740.8055-0.75010.38590.031-0.31070.5515-0.19540.605211.00258.25319.087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION1B1 - 106
3X-RAY DIFFRACTION2A120 - 213
4X-RAY DIFFRACTION2B107 - 210
5X-RAY DIFFRACTION3C8 - 110
6X-RAY DIFFRACTION4H1 - 122
7X-RAY DIFFRACTION4L1 - 107
8X-RAY DIFFRACTION5H123 - 213
9X-RAY DIFFRACTION5L108 - 210
10X-RAY DIFFRACTION6S4 - 107

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