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- PDB-5jw5: Structure of MEDI8852 Fab Fragment -

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Basic information

Entry
Database: PDB / ID: 5jw5
TitleStructure of MEDI8852 Fab Fragment
Components
  • MEDI8852 Heavy chain
  • MEDI8852 Light chain
KeywordsIMMUNE SYSTEM / Antibody Influenza
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNeu, U. / Collins, P.J. / Walker, P.A. / Vorlaender, M.K. / Ogrodowicz, R.W. / Martin, S.R. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Cell / Year: 2016
Title: Structure and Function Analysis of an Antibody Recognizing All Influenza A Subtypes.
Authors: Kallewaard, N.L. / Corti, D. / Collins, P.J. / Neu, U. / McAuliffe, J.M. / Benjamin, E. / Wachter-Rosati, L. / Palmer-Hill, F.J. / Yuan, A.Q. / Walker, P.A. / Vorlaender, M.K. / Bianchi, S. ...Authors: Kallewaard, N.L. / Corti, D. / Collins, P.J. / Neu, U. / McAuliffe, J.M. / Benjamin, E. / Wachter-Rosati, L. / Palmer-Hill, F.J. / Yuan, A.Q. / Walker, P.A. / Vorlaender, M.K. / Bianchi, S. / Guarino, B. / De Marco, A. / Vanzetta, F. / Agatic, G. / Foglierini, M. / Pinna, D. / Fernandez-Rodriguez, B. / Fruehwirth, A. / Silacci, C. / Ogrodowicz, R.W. / Martin, S.R. / Sallusto, F. / Suzich, J.A. / Lanzavecchia, A. / Zhu, Q. / Gamblin, S.J. / Skehel, J.J.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: MEDI8852 Heavy chain
L: MEDI8852 Light chain
A: MEDI8852 Heavy chain
B: MEDI8852 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0167
Polymers94,7314
Non-polymers2853
Water10,070559
1
H: MEDI8852 Heavy chain
L: MEDI8852 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5564
Polymers47,3662
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-36 kcal/mol
Surface area19770 Å2
MethodPISA
2
A: MEDI8852 Heavy chain
B: MEDI8852 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4613
Polymers47,3662
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-29 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.220, 109.920, 139.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21A
12L
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLYSLYSHA1 - 2291 - 227
21GLNGLNLYSLYSAC1 - 2291 - 227
12ASPASPGLUGLULB1 - 2091 - 209
22ASPASPGLUGLUBD1 - 2091 - 209

NCS ensembles :
ID
1
2

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Components

#1: Antibody MEDI8852 Heavy chain


Mass: 24455.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody MEDI8852 Light chain


Mass: 22910.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2 M Ammonium Dihydrogen Phosphate, seeded from crystals obtained from 18% PEG8000, 0.1 M Sodium Cacodylate pH 6.5 and 0.2 M Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97941 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 1.9→86.43 Å / Num. obs: 77785 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 31.51 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-1.950.7452.41198.4
1.95-20.5553.11198.8
2-2.060.5013.86198.3
2.06-2.120.424.52198.6
2.12-2.190.3535.28199
2.19-2.270.35.99198.9
2.27-2.360.256.73198.6
2.36-2.450.2157.15198.2
2.45-2.560.1768.56198.3
2.56-2.690.1479.88198.1
2.69-2.830.11511.66198
2.83-30.09413.51197.4
3-3.210.07315.96196.6
3.21-3.470.06518.49196
3.47-3.80.05820.76195.4
3.8-4.250.05421.94194.4
4.25-4.910.04922.74193.8
4.91-6.010.04823.19192.3
6.01-8.50.04722.92189.8
8.50.03925.59183.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0124refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HOT (chain B) 4KMT (chain L)

3hot

4kmt


Resolution: 1.9→86.43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.223 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.133
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 3842 4.9 %RANDOM
Rwork0.1866 ---
obs0.188 73943 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.03 Å2 / Biso mean: 29.378 Å2 / Biso min: 13.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--1.5 Å2-0 Å2
3----0.9 Å2
Refinement stepCycle: final / Resolution: 1.9→86.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6548 0 15 559 7122
Biso mean--55.94 33.72 -
Num. residues----862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026954
X-RAY DIFFRACTIONr_bond_other_d0.0050.026323
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9489514
X-RAY DIFFRACTIONr_angle_other_deg1.157314640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47124.265272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.563151103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4361531
X-RAY DIFFRACTIONr_chiral_restr0.0890.21073
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218037
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021586
X-RAY DIFFRACTIONr_mcbond_it1.7213.8713573
X-RAY DIFFRACTIONr_mcbond_other1.7013.8683572
X-RAY DIFFRACTIONr_mcangle_it2.5344.8584496
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11H24882
12A24882
21L22832
22B22832
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 265 -
Rwork0.298 5461 -
all-5726 -
obs--98.33 %
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)
11.9792-1.7347-0.01264.35980.43390.74630.08260.3397-0.0723-0.1507-0.0718-0.00780.0970.0374-0.01070.07170.0542-0.02090.1499-0.01580.130834.78711.960125.3854
24.5012-1.47571.9452.551-1.01073.3132-0.1597-0.13630.15930.15610.0157-0.1627-0.24930.48750.1440.0219-0.0328-0.00960.12640.01290.157439.544218.434453.005
31.9075-0.2076-0.1162.8985-0.62365.58190.02230.1679-0.3804-0.10150.06590.17270.2251-0.2206-0.08820.0192-0.0031-0.01490.0275-0.03320.244529.8534-12.707841.7574
41.441-0.1741-0.03965.2944-0.50021.91610.0382-0.20720.17490.19920.01630.2207-0.2634-0.1119-0.05450.06560.01230.01960.04420.00280.138426.904715.758963.8107
53.01771.8741-0.5082.3844-0.20680.8548-0.0306-0.1889-0.05390.0573-0.032-0.00690.0365-0.00140.06270.01190.0045-0.00320.03530.03130.11481.96057.303247.1247
64.93790.26823.09461.3970.66624.0866-0.08530.03140.2006-0.0987-0.04470.0989-0.3038-0.28880.130.03750.0347-0.0120.04560.01090.14212.867525.082120.8793
71.81911.22060.30022.88650.65024.56470.047-0.0867-0.2950.0033-0.0386-0.16840.17510.1381-0.00830.01170.00520.01490.01030.02760.18991.6167-7.624430.6673
81.64891.63440.1324.11380.88371.241-0.07660.1566-0.0293-0.18380.1431-0.1932-0.07930.0764-0.06650.0347-0.0117-0.00550.0203-0.00950.115413.506619.83979.008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 129
2X-RAY DIFFRACTION2A130 - 229
3X-RAY DIFFRACTION3B1 - 102
4X-RAY DIFFRACTION4B103 - 208
5X-RAY DIFFRACTION5H1 - 128
6X-RAY DIFFRACTION6H129 - 228
7X-RAY DIFFRACTION7L1 - 102
8X-RAY DIFFRACTION8L103 - 209

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