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- PDB-5n2k: Structure of unbound Briakinumab FAb -

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Basic information

Entry
Database: PDB / ID: 5n2k
TitleStructure of unbound Briakinumab FAb
Components
  • (Briakinumab FAb heavy ...) x 2
  • (Briakinumab FAb light ...) x 2
KeywordsIMMUNE SYSTEM / antagonist / antibody / extracellular region
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.219 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
VLAIO Belgium
Citation
Journal: Immunity / Year: 2018
Title: Structural Activation of Pro-inflammatory Human Cytokine IL-23 by Cognate IL-23 Receptor Enables Recruitment of the Shared Receptor IL-12R beta 1.
Authors: Bloch, Y. / Bouchareychas, L. / Merceron, R. / Skladanowska, K. / Van den Bossche, L. / Detry, S. / Govindarajan, S. / Elewaut, D. / Haerynck, F. / Dullaers, M. / Adamopoulos, I.E. / Savvides, S.N.
#1: Journal: To Be Published
Title: Human antibodies that bind human IL-12 and methods for producing
Authors: Salfeld, J. / Smith, S.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Briakinumab FAb light chain
B: Briakinumab FAb heavy chain
C: Briakinumab FAb light chain
D: Briakinumab FAb heavy chain
E: Briakinumab FAb light chain
F: Briakinumab FAb heavy chain
G: Briakinumab FAb light chain
H: Briakinumab FAb heavy chain
I: Briakinumab FAb light chain
J: Briakinumab FAb heavy chain
K: Briakinumab FAb light chain
L: Briakinumab FAb heavy chain
M: Briakinumab FAb light chain
N: Briakinumab FAb heavy chain
P: Briakinumab FAb heavy chain
O: Briakinumab FAb light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)453,18717
Polymers453,12516
Non-polymers621
Water18,1051005
1
A: Briakinumab FAb light chain
B: Briakinumab FAb heavy chain


Theoretical massNumber of molelcules
Total (without water)56,6452
Polymers56,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-26 kcal/mol
Surface area19630 Å2
MethodPISA
2
C: Briakinumab FAb light chain
D: Briakinumab FAb heavy chain


Theoretical massNumber of molelcules
Total (without water)56,6452
Polymers56,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-26 kcal/mol
Surface area20240 Å2
MethodPISA
3
E: Briakinumab FAb light chain
F: Briakinumab FAb heavy chain


Theoretical massNumber of molelcules
Total (without water)56,6452
Polymers56,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-22 kcal/mol
Surface area19140 Å2
MethodPISA
4
G: Briakinumab FAb light chain
H: Briakinumab FAb heavy chain


Theoretical massNumber of molelcules
Total (without water)56,6282
Polymers56,6282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-23 kcal/mol
Surface area18200 Å2
MethodPISA
5
I: Briakinumab FAb light chain
J: Briakinumab FAb heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6903
Polymers56,6282
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-23 kcal/mol
Surface area19290 Å2
MethodPISA
6
K: Briakinumab FAb light chain
L: Briakinumab FAb heavy chain


Theoretical massNumber of molelcules
Total (without water)56,6452
Polymers56,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-21 kcal/mol
Surface area19180 Å2
MethodPISA
7
M: Briakinumab FAb light chain
N: Briakinumab FAb heavy chain


Theoretical massNumber of molelcules
Total (without water)56,6452
Polymers56,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-22 kcal/mol
Surface area19020 Å2
MethodPISA
8
P: Briakinumab FAb heavy chain
O: Briakinumab FAb light chain


Theoretical massNumber of molelcules
Total (without water)56,6452
Polymers56,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-25 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.250, 172.540, 138.159
Angle α, β, γ (deg.)90.00, 106.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 4 types, 16 molecules ACEIKMOBDFHLNPGJ

#1: Antibody
Briakinumab FAb light chain


Mass: 25925.178 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: the secretion signal is cleaved off likely between residues 29 and 30
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Details (production host): transient transfection / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody
Briakinumab FAb heavy chain


Mass: 30719.658 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: The secretion signal is cleaved off likely between residues 29 and 30. The purification tag was removed by thrombin digest cleaving between residues 256 and 257.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Details (production host): transient transfection / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Antibody Briakinumab FAb light chain


Mass: 25908.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The secretion signal is cleaved off between residues29 and 30.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Details (production host): transient transfection / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Antibody Briakinumab FAb heavy chain


Mass: 30702.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The secretion signal is cleaved off between residues 29 and 30. The purification tag was removed by thrombin digest cleaving between residues 256 and 257.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Details (production host): transient transfection / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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Non-polymers , 2 types, 1006 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1005 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: Microseed matrix screen. Seed stock 22% (w/v) PEG 3350, 40 mM Glycine. Mother liquor 200 mM NH4I, 20% (w/v) PEG 3350.
PH range: 6.2-9.5
Temp details: Molecular Dimensions cooled crystallization incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.219→82.44 Å / Num. obs: 178979 / % possible obs: 94.7 % / Redundancy: 4.09 % / Biso Wilson estimate: 53.45 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.11 / Net I/σ(I): 8.85
Reflection shellResolution: 2.219→2.34 Å / Redundancy: 4.11 % / Mean I/σ(I) obs: 2.17 / Num. unique obs: 26837 / CC1/2: 0.686 / Rrim(I) all: 0.917 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Separate constant and variable domains coming from Modeller

Resolution: 2.219→81.884 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 2153 1.21 %
Rwork0.204 --
obs0.2044 178458 94.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.219→81.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25107 0 4 1005 26116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326002
X-RAY DIFFRACTIONf_angle_d0.59835561
X-RAY DIFFRACTIONf_dihedral_angle_d8.35315504
X-RAY DIFFRACTIONf_chiral_restr0.0454019
X-RAY DIFFRACTIONf_plane_restr0.0034565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2192-2.27090.34041460.288811599X-RAY DIFFRACTION93
2.2709-2.32760.27661390.264311940X-RAY DIFFRACTION97
2.3276-2.39060.29431480.256611976X-RAY DIFFRACTION97
2.3906-2.46090.28991440.249711969X-RAY DIFFRACTION97
2.4609-2.54040.27121410.239911960X-RAY DIFFRACTION96
2.5404-2.63120.26241420.23911932X-RAY DIFFRACTION96
2.6312-2.73650.29061580.230211900X-RAY DIFFRACTION96
2.7365-2.86110.26081410.230811819X-RAY DIFFRACTION95
2.8611-3.01190.24911440.224711789X-RAY DIFFRACTION95
3.0119-3.20060.2541380.2311725X-RAY DIFFRACTION94
3.2006-3.44780.24311440.211311669X-RAY DIFFRACTION94
3.4478-3.79470.2421410.197211590X-RAY DIFFRACTION93
3.7947-4.34380.20891440.172311566X-RAY DIFFRACTION93
4.3438-5.47260.17331420.15411499X-RAY DIFFRACTION92
5.4726-81.93940.21181410.194911372X-RAY DIFFRACTION90
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)
13.7501-0.30580.55575.92910.71512.4314-0.0726-0.20180.7826-0.1677-0.0813-0.01-0.2202-0.00020.12860.1884-0.026-0.01210.31470.01530.3961-37.685581.1642-67.0057
24.5345-1.25462.53221.2049-1.20217.46580.04830.66160.1309-0.313-0.2609-0.07150.12470.16810.1730.29990.02430.02250.32150.07250.2417-46.342362.7281-91.6854
34.81990.90751.08583.25861.30931.7763-0.0709-0.87030.7580.1026-0.00160.0827-0.0697-0.2360.08580.22330.0328-0.0450.432-0.07580.5249-59.165285.5056-67.5759
46.7682-1.33810.37523.8750.18013.57080.07680.0774-1.4874-0.0503-0.1219-0.1660.86810.17330.06370.4037-0.0013-0.00780.31460.00970.6781-58.259451.8891-88.7687
56.1936-1.5303-0.35275.2263-0.88343.2976-0.02890.0117-0.30280.16130.0804-0.0228-0.08640.0417-0.0440.2917-0.01430.01260.31110.01570.1589-77.8984-17.9017-11.9302
65.22382.5467-1.60293.8318-2.51443.29720.07780.4566-0.002-1.0794-0.0542-0.6340.23480.1496-0.03740.9270.01960.25730.58190.13680.5533-68.25323.2783-30.7066
73.26380.38610.29186.8723-1.4743.75550.18680.01430.13990.5397-0.0159-0.3951-0.24810.384-0.16640.3411-0.0551-0.04450.375-0.00530.2978-61.3825-8.9-0.0325
83.7074-0.04051.61282.5602-0.94223.15690.1207-0.15150.0353-0.0255-0.2309-0.1546-0.3614-0.11250.0641.0222-0.09260.31090.64290.15770.8214-67.717919.7006-26.2498
91.8128-1.15630.15921.16110.54491.0811.47320.52290.28230.5391-0.2259-0.005-0.1873-1.0086-0.92140.7757-0.07770.32220.55790.11550.9417-61.945515.8428-51.5876
101.8740.9355-0.04664.4557-1.7792.86160.01090.2023-0.3457-0.0657-0.1151-0.02210.2343-0.04220.0940.2465-0.03580.01140.2919-0.00120.3521-16.067826.6917-80.0044
116.76453.1763-0.66844.7662-0.59164.9565-0.35421.06-0.3993-0.55570.4503-0.1502-0.00380.1608-0.12280.3912-0.05360.00360.5341-0.01030.3027-3.730447.4689-95.7812
122.03111.23010.61286.2859-1.53032.87110.4877-0.4762-0.26830.9204-0.3735-0.48320.05560.0526-0.07280.4393-0.1237-0.08860.39030.08060.44640.467932.4834-65.2775
134.9440.25981.25884.6134-1.23224.9341-0.14680.40351.3411-0.32230.18240.83-0.8216-0.34620.05360.5059-0.0106-0.0230.36650.13730.8191-5.546562.9458-89.9912
142.59830.9443-0.244.46071.17762.1294-0.05640.00510.02040.3235-0.03320.00510.26080.19090.08790.30420.06540.00010.36750.07180.3205-13.225-2.90145.602
152.11411.88840.17161.964-0.21264.671.0747-1.62950.37011.8354-1.19720.2624-0.12780.0322-0.08671.2197-0.49270.11951.0936-0.00910.3911-17.608710.025630.0784
164.295-0.3487-1.24465.3842.01824.11080.16530.10620.27060.31250.03480.7996-0.2255-0.6053-0.07740.32620.02220.11220.39490.08460.4743-34.5817-10.16568.9776
177.63392.16970.80651.6669-0.6850.85280.31470.75082.68230.8762-0.56230.8886-0.0521-0.18840.1821.23310.03220.76030.9511-0.13561.9391-31.336819.858228.6356
181.3947-0.0196-0.5332.431.67291.5917-0.1337-0.0484-0.410.3089-0.03790.02630.24160.02840.15380.28710.0012-0.00420.31990.11780.4074-36.781736.8889-59.7823
192.78780.427-1.92912.146-2.28515.8251-0.1486-0.2271-0.05210.06910.03310.05970.24660.18550.11690.4174-0.0125-0.02970.3077-0.01020.2542-41.867850.7489-34.7345
203.53330.2216-0.27334.87052.09262.11350.0344-0.00350.08080.6576-0.23291.14140.2084-0.47130.27760.416-0.06820.20710.39150.01280.7383-57.763330.2797-56.4991
212.89230.0464-0.71265.37750.47516.0141-0.27430.55720.9072-0.2668-0.27330.9602-1.0739-0.4810.44160.50720.0895-0.17160.51180.10820.6743-54.000361.4581-36.9457
221.35-0.7693-0.00617.702-2.14182.601-0.1033-0.51410.01410.3860.0342-0.182-0.13790.04140.03350.26770.0025-0.07660.46660.04950.3208-75.477148.317611.4176
231.7686-0.7032-0.6534.5087-0.1411.366-0.2377-0.5887-0.081.57490.1679-1.0290.23720.41390.09050.92040.1231-0.22690.78950.2450.9601-65.596718.123323.4122
243.1663-0.5148-1.75975.4241-0.62242.96220.0470.0121-0.51-0.3084-0.08710.2690.1161-0.1072-0.04430.26760.0127-0.03820.28020.00450.3566-62.32542.804-6.5907
257.57722.2231-4.23578.2406-5.14064.3455-0.59870.243-0.2775-0.93430.1596-0.78651.0795-0.54430.50290.7305-0.03740.06070.76290.12730.8-70.843912.21979.0156
263.1417-0.3818-1.50345.19871.05963.04880.0710.42650.0732-0.1894-0.21420.143-0.2497-0.17320.12770.20560.0116-0.07480.35040.01520.3083-32.31515.3145-78.0865
273.34733.8936-2.42219.1606-0.98432.5436-0.24160.49110.2784-0.9095-0.02481.59280.2665-0.6410.35740.5694-0.0554-0.09440.9462-0.27450.9973-41.3833-26.2285-91.8963
283.14790.9261-1.544.06480.17031.9343-0.1132-0.0026-0.69410.0807-0.04270.24320.09610.09940.07930.2616-0.03590.02630.3702-0.02540.6121-45.9475-2.4125-61.3513
293.41490.1668-2.28064.02613.20537.1718-0.6035-0.41180.3471.088-0.48511.43541.10771.59690.63870.7273-0.05870.26481.1762-0.11620.9134-38.0645-32.9835-77.4858
303.2071-1.03470.25577.1021-0.20712.3978-0.0365-0.01090.3597-0.25280.0051-0.669-0.17990.09580.03770.2217-0.00710.07160.38070.04620.3505-13.539838.7614-0.8051
311.85020.2149-0.0232.04720.14831.43980.17591.99390.0818-1.3258-0.59260.1005-0.3328-0.00990.2180.99240.3601-0.0891.44150.09840.3665-21.453422.6137-25.6184
324.6003-0.26641.68972.66740.14842.28160.0043-0.41950.30090.1724-0.0113-0.02420.0005-0.1211-0.01690.28290.04720.06620.39870.01840.2428-34.606845.369-0.054
330.44510.3392-0.2461.77510.01030.59980.45851.1185-1.2112-0.6948-0.2740.51430.4403-0.12920.06440.94880.3403-0.47081.1714-0.6181.1344-35.247114.1301-22.8671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 111 )
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 216 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 121 )
4X-RAY DIFFRACTION4chain 'B' and (resid 122 through 218 )
5X-RAY DIFFRACTION5chain 'C' and (resid 2 through 105 )
6X-RAY DIFFRACTION6chain 'C' and (resid 106 through 216 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 121 )
8X-RAY DIFFRACTION8chain 'D' and (resid 122 through 212 )
9X-RAY DIFFRACTION9chain 'D' and (resid 213 through 228 )
10X-RAY DIFFRACTION10chain 'E' and (resid 1 through 123 )
11X-RAY DIFFRACTION11chain 'E' and (resid 124 through 214 )
12X-RAY DIFFRACTION12chain 'F' and (resid 1 through 121 )
13X-RAY DIFFRACTION13chain 'F' and (resid 122 through 216 )
14X-RAY DIFFRACTION14chain 'G' and (resid 1 through 123 )
15X-RAY DIFFRACTION15chain 'G' and (resid 124 through 213 )
16X-RAY DIFFRACTION16chain 'H' and (resid 1 through 121 )
17X-RAY DIFFRACTION17chain 'H' and (resid 122 through 215 )
18X-RAY DIFFRACTION18chain 'I' and (resid 1 through 123 )
19X-RAY DIFFRACTION19chain 'I' and (resid 124 through 214 )
20X-RAY DIFFRACTION20chain 'J' and (resid 1 through 120 )
21X-RAY DIFFRACTION21chain 'J' and (resid 121 through 217 )
22X-RAY DIFFRACTION22chain 'K' and (resid 2 through 123 )
23X-RAY DIFFRACTION23chain 'K' and (resid 124 through 215 )
24X-RAY DIFFRACTION24chain 'L' and (resid 1 through 121 )
25X-RAY DIFFRACTION25chain 'L' and (resid 122 through 215 )
26X-RAY DIFFRACTION26chain 'M' and (resid 2 through 118 )
27X-RAY DIFFRACTION27chain 'M' and (resid 119 through 213 )
28X-RAY DIFFRACTION28chain 'N' and (resid 1 through 121 )
29X-RAY DIFFRACTION29chain 'N' and (resid 122 through 215 )
30X-RAY DIFFRACTION30chain 'O' and (resid 1 through 111 )
31X-RAY DIFFRACTION31chain 'O' and (resid 112 through 213 )
32X-RAY DIFFRACTION32chain 'P' and (resid 1 through 108 )
33X-RAY DIFFRACTION33chain 'P' and (resid 109 through 216 )

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