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- PDB-4cni: Crystal structure of the Fab portion of Olokizumab in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4cni
TitleCrystal structure of the Fab portion of Olokizumab in complex with IL- 6
Components
  • INTERLEUKIN-6
  • OLOKIZUMAB HEAVY CHAIN, FAB PORTION
  • OLOKIZUMAB LIGHT CHAIN, FAB PORTION
KeywordsIMMUNE SYSTEM / CDP6038 / INTERLEUKIN 6
Function / homology
Function and homology information


regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / germinal center B cell differentiation / interleukin-6 receptor complex ...regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / germinal center B cell differentiation / interleukin-6 receptor complex / positive regulation of type B pancreatic cell apoptotic process / positive regulation of apoptotic DNA fragmentation / hepatocyte proliferation / positive regulation of extracellular matrix disassembly / regulation of microglial cell activation / response to peptidoglycan / neutrophil apoptotic process / interleukin-6 receptor binding / positive regulation of B cell activation / positive regulation of receptor signaling pathway via STAT / T-helper 17 cell lineage commitment / inflammatory response to wounding / positive regulation of T-helper 2 cell cytokine production / negative regulation of collagen biosynthetic process / endocrine pancreas development / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / vascular endothelial growth factor production / positive regulation of neuroinflammatory response / T follicular helper cell differentiation / negative regulation of chemokine production / positive regulation of leukocyte chemotaxis / neutrophil mediated immunity / positive regulation of platelet aggregation / cell surface receptor signaling pathway via STAT / positive regulation of cytokine production involved in inflammatory response / negative regulation of bone resorption / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / Interleukin-6 signaling / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immunoglobulin production / MAPK3 (ERK1) activation / interleukin-6-mediated signaling pathway / negative regulation of fat cell differentiation / maintenance of blood-brain barrier / MAPK1 (ERK2) activation / Interleukin-10 signaling / positive regulation of interleukin-17 production / monocyte chemotaxis / humoral immune response / positive regulation of interleukin-10 production / Transcriptional Regulation by VENTX / negative regulation of lipid storage / positive regulation of vascular endothelial growth factor production / cell surface receptor signaling pathway via JAK-STAT / regulation of angiogenesis / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / response to glucocorticoid / positive regulation of T cell proliferation / positive regulation of chemokine production / positive regulation of peptidyl-serine phosphorylation / positive regulation of glial cell proliferation / regulation of insulin secretion / positive regulation of DNA-binding transcription factor activity / liver regeneration / positive regulation of interleukin-1 beta production / positive regulation of translation / cytokine activity / acute-phase response / response to activity / positive regulation of interleukin-8 production / positive regulation of receptor signaling pathway via JAK-STAT / Post-translational protein phosphorylation / positive regulation of smooth muscle cell proliferation / growth factor activity / cytokine-mediated signaling pathway / cellular response to virus / positive regulation of miRNA transcription / platelet activation / negative regulation of neurogenesis / positive regulation of interleukin-6 production / cellular response to hydrogen peroxide / neuron cellular homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / positive regulation of tumor necrosis factor production / ADORA2B mediated anti-inflammatory cytokines production / glucose homeostasis / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / defense response to virus / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / positive regulation of apoptotic process / inflammatory response / endoplasmic reticulum lumen
Similarity search - Function
Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins ...Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShaw, S. / Bourne, T. / Meier, C. / Carrington, B. / Gelinas, R. / Henry, A. / Popplewell, A. / Adams, R. / Baker, T. / Rapecki, S. ...Shaw, S. / Bourne, T. / Meier, C. / Carrington, B. / Gelinas, R. / Henry, A. / Popplewell, A. / Adams, R. / Baker, T. / Rapecki, S. / Marshall, D. / Neale, H. / Lawson, A.
CitationJournal: Mabs / Year: 2014
Title: Discovery and Characterization of Olokizumab: A Humanized Antibody Targeting Interleukin-6 and Neutralizing Gp130-Signaling.
Authors: Shaw, S. / Bourne, T. / Meier, C. / Carrington, B. / Gelinas, R. / Henry, A. / Popplewell, A. / Adams, R. / Baker, T. / Rapecki, S. / Marshall, D. / Moore, A. / Neale, H. / Lawson, A.
History
DepositionJan 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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
A: OLOKIZUMAB HEAVY CHAIN, FAB PORTION
B: OLOKIZUMAB LIGHT CHAIN, FAB PORTION
C: INTERLEUKIN-6
D: INTERLEUKIN-6
H: OLOKIZUMAB HEAVY CHAIN, FAB PORTION
L: OLOKIZUMAB LIGHT CHAIN, FAB PORTION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,59013
Polymers133,7846
Non-polymers8077
Water28,5901587
1
A: OLOKIZUMAB HEAVY CHAIN, FAB PORTION
B: OLOKIZUMAB LIGHT CHAIN, FAB PORTION
D: INTERLEUKIN-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2476
Polymers66,8923
Non-polymers3553
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-39.4 kcal/mol
Surface area33780 Å2
MethodPQS
2
C: INTERLEUKIN-6
H: OLOKIZUMAB HEAVY CHAIN, FAB PORTION
L: OLOKIZUMAB LIGHT CHAIN, FAB PORTION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3437
Polymers66,8923
Non-polymers4514
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-39.9 kcal/mol
Surface area34040 Å2
MethodPQS
Unit cell
Length a, b, c (Å)241.988, 241.988, 76.591
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

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Protein , 1 types, 2 molecules CD

#3: Protein INTERLEUKIN-6 / IL-6 / B-CELL STIMULATORY FACTOR 2 / BSF-2 / CTL DIFFERENTIATION FACTOR / CDF / HYBRIDOMA GROWTH ...IL-6 / B-CELL STIMULATORY FACTOR 2 / BSF-2 / CTL DIFFERENTIATION FACTOR / CDF / HYBRIDOMA GROWTH FACTOR / INTERFERON BETA-2 / IFN-BETA-2


Mass: 19670.518 Da / Num. of mol.: 2 / Fragment: RESIDUES 41-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05231

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Antibody , 2 types, 4 molecules AHBL

#1: Antibody OLOKIZUMAB HEAVY CHAIN, FAB PORTION


Mass: 23940.588 Da / Num. of mol.: 2 / Fragment: FAB PORTION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY
#2: Antibody OLOKIZUMAB LIGHT CHAIN, FAB PORTION


Mass: 23280.766 Da / Num. of mol.: 2 / Fragment: FAB PORTION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY

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Non-polymers , 3 types, 1594 molecules

#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1587 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.84 Å3/Da / Density % sol: 74.58 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 126842 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.2 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.971 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21549 6411 5.1 %RANDOM
Rwork0.17608 ---
obs0.17807 120388 97.51 %-
Displacement parametersBiso mean: 22.986 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20.64 Å20 Å2
2--1.28 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9323 0 47 1587 10957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229616
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.96113067
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73751221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28424.928416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.756151617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6341543
X-RAY DIFFRACTIONr_chiral_restr0.0760.21468
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217219
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.93126056
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8839786
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.02453560
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.62263272
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 494 -
Rwork0.229 8770 -
obs--97.32 %

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