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- PDB-7z2m: Crystal Structure of the 11.003 Fab in complex with human IL-17A -

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Basic information

Entry
Database: PDB / ID: 7z2m
TitleCrystal Structure of the 11.003 Fab in complex with human IL-17A
Components
  • 11.003 Fab heavy-chain
  • 11.003 Fab light-chain
  • Interleukin-17A
KeywordsIMMUNE SYSTEM / Immunoglobulin / Cytokine / IL-17A
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / fibroblast activation / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / cytokine activity / response to wounding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cell-cell signaling / gene expression / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / immune response / protein heterodimerization activity / external side of plasma membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine-knot cytokine
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.899 Å
AuthorsRondeau, J.M. / Lehmann, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2023
Title: "Redirecting an anti-IL-1 beta antibody to bind a new, unrelated and computationally predicted epitope on hIL-17A".
Authors: Fischman, S. / Levin, I. / Rondeau, J.M. / Strajbl, M. / Lehmann, S. / Huber, T. / Nimrod, G. / Cebe, R. / Omer, D. / Kovarik, J. / Bernstein, S. / Sasson, Y. / Demishtein, A. / Shlamkovich, ...Authors: Fischman, S. / Levin, I. / Rondeau, J.M. / Strajbl, M. / Lehmann, S. / Huber, T. / Nimrod, G. / Cebe, R. / Omer, D. / Kovarik, J. / Bernstein, S. / Sasson, Y. / Demishtein, A. / Shlamkovich, T. / Bluvshtein, O. / Grossman, N. / Barak-Fuchs, R. / Zhenin, M. / Fastman, Y. / Twito, S. / Vana, T. / Zur, N. / Ofran, Y.
History
DepositionFeb 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 11.003 Fab light-chain
B: 11.003 Fab heavy-chain
C: 11.003 Fab light-chain
D: 11.003 Fab heavy-chain
E: 11.003 Fab light-chain
F: 11.003 Fab heavy-chain
G: Interleukin-17A
H: 11.003 Fab heavy-chain
I: Interleukin-17A
J: Interleukin-17A
K: Interleukin-17A
L: 11.003 Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,77715
Polymers247,50112
Non-polymers2763
Water27,1491507
1
A: 11.003 Fab light-chain
B: 11.003 Fab heavy-chain
E: 11.003 Fab light-chain
F: 11.003 Fab heavy-chain
J: Interleukin-17A
K: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,9358
Polymers123,7506
Non-polymers1842
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 11.003 Fab light-chain
D: 11.003 Fab heavy-chain
G: Interleukin-17A
H: 11.003 Fab heavy-chain
I: Interleukin-17A
L: 11.003 Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8437
Polymers123,7506
Non-polymers921
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.996, 107.335, 269.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody
11.003 Fab light-chain


Mass: 23640.256 Da / Num. of mol.: 4 / Fragment: Fab light-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
11.003 Fab heavy-chain


Mass: 24115.092 Da / Num. of mol.: 4 / Fragment: Fab heavy-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein
Interleukin-17A / IL-17 / IL-17A / Cytotoxic T-lymphocyte-associated antigen 8 / CTLA-8


Mass: 14119.862 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T1 / References: UniProt: Q16552
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1507 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium potassium tartrate, 20% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999802 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2020 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999802 Å / Relative weight: 1
ReflectionResolution: 1.899→134.649 Å / Num. obs: 190056 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 38.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.045 / Rrim(I) all: 0.138 / Net I/av σ(I): 11.1 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.899-1.90510.92.782035918690.3270.9132.931.198.2
8.811-134.6499.40.0342024421500.9990.0110.03637.299.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.01 Å134.76 Å
Translation2.01 Å134.76 Å

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Processing

Software
NameVersionClassification
XDSJan 31, 2020data reduction
AimlessCCP4-7.0data scaling
PHASER2.8.3phasing
BUSTER2.11.7 (20-MAY-2020)refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HR9

4hr9


Resolution: 1.899→134.649 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 9498 5.04 %RANDOM
Rwork0.2013 ---
obs0.2026 188538 98 %-
Displacement parametersBiso max: 100.32 Å2 / Biso mean: 41.45 Å2 / Biso min: 20.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.7758 Å20 Å20 Å2
2---3.2424 Å20 Å2
3---1.4666 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.899→134.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16443 0 18 1507 17968
Biso mean--46.43 46.63 -
Num. residues----2124
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5597SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2820HARMONIC5
X-RAY DIFFRACTIONt_it17021HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2219SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14383SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d17021HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg23202HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.9
X-RAY DIFFRACTIONt_other_torsion15.12
LS refinement shellResolution: 1.9→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2268 206 5.46 %
Rwork0.2079 3565 -
all0.2089 3771 -
obs--85.63 %
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)
10.18230.1025-0.07260.14070.10280.86250.0198-0.0393-0.0234-0.02340.0382-0.06370.0348-0.0777-0.05810.03470.00640.011-0.11420.00820.000816.7561-13.956727.0103
20.03150.03530.64440.3636-0.17921.9823-0.04940.02330.0439-0.0345-0.0138-0.0239-0.050.16270.0632-0.01310.00990.0076-0.0640.0134-0.011929.7466-3.348528.8735
300.04040.16460.4101-0.33311.17330.06290.0718-0.04490.02150.00150.01360.0730.1015-0.0644-0.0310.0284-0.0037-0.0645-0.00180.0056-8.6953-27.289275.1046
40.0043-0.00820.43260.263-0.14552.58860.0309-0.00770.06870.03810.02840.0093-0.0481-0.2261-0.0593-0.02350.02920.013-0.0568-0.0032-0.0253-25.092-21.750474.0034
50.1204-0.16160.55150.4078-0.312.24210.04780.21050.01920.14790.0217-0.00160.10480.4424-0.06950.01470.0099-0.0035-0.0634-0.0302-0.080234.4527-29.7636115.189
60.0626-0.14820.39190.24340.02872.01360.05630.06620.02980.12710.08710.1019-0.0908-0.0054-0.14340.1199-0.01510.0501-0.1729-0.0035-0.040318.2374-21.9639114.412
70.5463-0.7785-0.60783.20910.30451.40570.0478-0.10480.0448-0.15970.0307-0.0191-0.0471-0.0641-0.07850.01440.0084-0.0058-0.09790.0027-0.0606-19.5304-13.048535.6186
80.11850.05780.44140.355-0.10362.018-0.0010.03140.02460.0009-0.00020.0553-0.12710.23140.00110.0433-0.0113-0.0112-0.097-0.0043-0.0593-11.1126-4.1262-12.8847
90.1078-0.4316-0.33493.0073-0.05941.02170.0065-0.0515-0.0244-0.0231-0.0330.035-0.11610.10670.02650.04830.0025-0.0091-0.1114-0.021-0.0588-13.0177-9.354727.7804
100.491-0.6976-0.51984.29110.63041.60790.0511-0.02590.0270.20250.0707-0.0222-0.0687-0.0583-0.12180.03520.0240.0031-0.121-0.0079-0.073920.597-12.565177.3997
110.13140.0838-0.22874.09220.52261.1273-0.0106-0.07930.02660.08470.02790.005500.0676-0.01730.01770.0352-0.0141-0.0829-0.0306-0.058327.3863-10.343167.4129
120.05260.2551-0.04970.36560.24571.6217-0.0167-0.01710.0126-0.0015-0.02750.01560.1328-0.01830.04420.05460.00460.0047-0.1321-0.009-0.0346-23.0059-16.2825-14.8473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 213
2X-RAY DIFFRACTION2{ B|* }B1 - 219
3X-RAY DIFFRACTION3{ C|* }C1 - 213
4X-RAY DIFFRACTION4{ D|* }D1 - 220
5X-RAY DIFFRACTION5{ E|* }E1 - 214
6X-RAY DIFFRACTION6{ F|* }F1 - 219
7X-RAY DIFFRACTION7{ G|* }G19 - 131
8X-RAY DIFFRACTION8{ H|* }H1 - 221
9X-RAY DIFFRACTION9{ I|* }I20 - 126
10X-RAY DIFFRACTION10{ J|* }J18 - 128
11X-RAY DIFFRACTION11{ K|* }K21 - 126
12X-RAY DIFFRACTION12{ L|* }L1 - 213

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