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- PDB-6ppg: Crystal structure of IL17FF bound to Fab fragments of MCAF5352A -

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Basic information

Entry
Database: PDB / ID: 6ppg
TitleCrystal structure of IL17FF bound to Fab fragments of MCAF5352A
Components
  • (Fab MCAF5352A ...) x 2
  • Interleukin-17F
KeywordsCYTOKINE / IL-17 / complex
Function / homology
Function and homology information


regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / positive regulation of lymphotoxin A production / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / regulation of transforming growth factor beta receptor signaling pathway / cytokine receptor binding ...regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / positive regulation of lymphotoxin A production / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / regulation of transforming growth factor beta receptor signaling pathway / cytokine receptor binding / positive regulation of cytokine production involved in inflammatory response / cartilage development / regulation of interleukin-6 production / cytokine binding / negative regulation of angiogenesis / positive regulation of cytokine production / cytokine activity / positive regulation of interleukin-6 production / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / protein heterodimerization activity / innate immune response / 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 Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsHuang, C.S. / Yin, J.P. / Hymowitz, S.G.
CitationJournal: Mabs
Title: Dissecting the molecular basis of high viscosity of monospecific and bispecific IgG antibodies.
Authors: Tilegenova, C. / Izadi, S. / Yin, J. / Huang, C.S. / Wu, J. / Ellerman, D. / Hymowitz, S.G. / Walters, B. / Salisbury, C. / Carter, P.J.
History
DepositionJul 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Interleukin-17F
A: Fab MCAF5352A light chain
B: Fab MCAF5352A heavy chain
H: Fab MCAF5352A heavy chain
L: Fab MCAF5352A light chain
G: Interleukin-17F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,44561
Polymers125,0446
Non-polymers6,40055
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23050 Å2
ΔGint-388 kcal/mol
Surface area46900 Å2
Unit cell
Length a, b, c (Å)103.820, 103.820, 243.327
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-301-

CD

21A-316-

CD

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Components

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Antibody , 2 types, 4 molecules ALBH

#2: Antibody Fab MCAF5352A light chain


Mass: 23533.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab MCAF5352A heavy chain


Mass: 24066.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Sugars , 2 types, 4 molecules FG

#1: Protein Interleukin-17F / IL-17F / Cytokine ML-1


Mass: 14922.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17F / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96PD4
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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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Non-polymers , 2 types, 202 molecules

#5: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 53 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate pH 4.6, 0.1M cadmium chloride, 30% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.75→47.79 Å / Num. obs: 40672 / % possible obs: 99.9 % / Redundancy: 8.3 % / Net I/σ(I): 2.6
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 7.6 % / Num. unique obs: 3977 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jpy

1jpy


Resolution: 2.75→47.79 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.878 / SU B: 14.646 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.857 / ESU R Free: 0.362
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2061 5.1 %RANDOM
Rwork0.2243 ---
obs0.2269 38260 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 205.9 Å2 / Biso mean: 51.73 Å2 / Biso min: 7.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å20 Å2
2---0.46 Å20 Å2
3---1.5 Å2
Refinement stepCycle: final / Resolution: 2.75→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8203 0 80 149 8432
Biso mean--108.02 40.1 -
Num. residues----1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138497
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177341
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.64411533
X-RAY DIFFRACTIONr_angle_other_deg1.1111.56817035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20851095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55422.653377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.305151213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9451541
X-RAY DIFFRACTIONr_chiral_restr0.0380.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029629
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021766
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 153 -
Rwork0.378 2775 -
all-2928 -
obs--99.97 %

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