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- PDB-6z7z: Porcine insulin in complex with the analytical antibody OXI-005 Fab -

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Basic information

Entry
Database: PDB / ID: 6z7z
TitlePorcine insulin in complex with the analytical antibody OXI-005 Fab
Components
  • (Insulin) x 2
  • OXI-005 Fab Heavy chain
  • OXI-005 Fab Light chain
KeywordsHORMONE / complex / insulin / analytical antibody / Fab
Function / homology
Function and homology information


positive regulation of lipoprotein lipase activity / Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process ...positive regulation of lipoprotein lipase activity / Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / lactate biosynthetic process / positive regulation of glucose metabolic process / positive regulation of fatty acid biosynthetic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / lipid biosynthetic process / positive regulation of respiratory burst / negative regulation of acute inflammatory response / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of mitotic nuclear division / positive regulation of glycolytic process / positive regulation of cytokine production / positive regulation of DNA replication / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / wound healing / hormone activity / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / vasodilation / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / protease binding / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Immunoglobulins / Immunoglobulin-like ...Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsJohansson, E.
CitationJournal: Protein Sci. / Year: 2021
Title: Insulin binding to the analytical antibody sandwich pair OXI-005 and HUI-018: Epitope mapping and binding properties.
Authors: Johansson, E. / Wu, X. / Yu, B. / Yang, Z. / Cao, Z. / Wiberg, C. / Jeppesen, C.B. / Poulsen, F.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OXI-005 Fab Light chain
B: OXI-005 Fab Heavy chain
C: OXI-005 Fab Light chain
D: OXI-005 Fab Heavy chain
E: Insulin
F: Insulin
G: Insulin
H: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,21710
Polymers106,1698
Non-polymers492
Water6,828379
1
A: OXI-005 Fab Light chain
B: OXI-005 Fab Heavy chain
G: Insulin
H: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1095
Polymers53,0844
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: OXI-005 Fab Light chain
D: OXI-005 Fab Heavy chain
E: Insulin
F: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1095
Polymers53,0844
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.670, 171.550, 83.170
Angle α, β, γ (deg.)90.000, 135.886, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPASNASNchain 'A'AA1 - 2111 - 211
221ASPASPASNASNchain 'C'CC1 - 2111 - 211
132GLUGLUPROPRO(chain 'B' and (resid 1 through 143 or resid 145 through 216))BB1 - 1301 - 130
142ASNASNLEULEU(chain 'B' and (resid 1 through 143 or resid 145 through 216))BB137 - 142137 - 142
152LEULEUPROPRO(chain 'B' and (resid 1 through 143 or resid 145 through 216))BB145 - 216145 - 216
262GLUGLUPROPRO(chain 'D' and (resid 1 through 130 or resid 137 through 143 or resid 145 through 216))DD1 - 1301 - 130
272ASNASNLEULEU(chain 'D' and (resid 1 through 130 or resid 137 through 143 or resid 145 through 216))DD137 - 142137 - 142
282LEULEUPROPRO(chain 'D' and (resid 1 through 130 or resid 137 through 143 or resid 145 through 216))DD145 - 216145 - 216
193GLYGLYASNASNchain 'E'EE1 - 211 - 21
2103GLYGLYASNASNchain 'G'GG1 - 211 - 21
1114ASNASNALAALA(chain 'F' and resid 3 through 30)FF3 - 303 - 30
2124ASNASNALAALAchain 'H'HH3 - 303 - 30

NCS ensembles :
ID
1
2
3
4

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Components

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Protein/peptide , 2 types, 4 molecules EGFH

#3: Protein/peptide Insulin


Mass: 2383.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01315
#4: Protein/peptide Insulin


Mass: 3403.927 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01315

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody OXI-005 Fab Light chain


Mass: 23539.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody OXI-005 Fab Heavy chain


Mass: 23757.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Non-polymers , 2 types, 381 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium chloride, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→47.99 Å / Num. obs: 41390 / % possible obs: 99.24 % / Redundancy: 3.4 % / Biso Wilson estimate: 41.98 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.1424 / Rpim(I) all: 0.09004 / Rrim(I) all: 0.1689 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.082 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 13981 / CC1/2: 0.46 / CC star: 0.794 / Rpim(I) all: 0.6723 / Rrim(I) all: 1.277 / % possible all: 97.45

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Processing

Software
NameVersionClassification
PHENIXdev_3714refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6Z7Y

6z7y


Resolution: 2.4→47.99 Å / SU ML: 0.4236 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 30.1053
RfactorNum. reflection% reflection
Rfree0.2588 2887 3.66 %
Rwork0.2102 --
obs0.212 41399 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7318 0 2 379 7699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00847502
X-RAY DIFFRACTIONf_angle_d1.125510210
X-RAY DIFFRACTIONf_chiral_restr0.05721143
X-RAY DIFFRACTIONf_plane_restr0.00731301
X-RAY DIFFRACTIONf_dihedral_angle_d20.83942686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.41821290.35393364X-RAY DIFFRACTION88.95
2.44-2.480.37741570.34273647X-RAY DIFFRACTION96.26
2.48-2.530.39171450.31263616X-RAY DIFFRACTION96.16
2.53-2.580.34111080.31243669X-RAY DIFFRACTION96.25
2.58-2.630.36911410.31163635X-RAY DIFFRACTION96.18
2.63-2.680.34541550.30813686X-RAY DIFFRACTION96.39
2.68-2.750.37971120.30053627X-RAY DIFFRACTION96.47
2.75-2.820.32871280.27553683X-RAY DIFFRACTION96.63
2.82-2.890.31281600.25743633X-RAY DIFFRACTION96.74
2.89-2.980.3031400.24093707X-RAY DIFFRACTION96.95
2.98-3.070.28521260.24913481X-RAY DIFFRACTION92.42
3.07-3.180.29491370.23183581X-RAY DIFFRACTION94.15
3.18-3.310.29231430.2263457X-RAY DIFFRACTION92.52
3.31-3.460.23191340.19773728X-RAY DIFFRACTION98.02
3.46-3.640.2451420.19863734X-RAY DIFFRACTION98.3
3.64-3.870.23671360.19053647X-RAY DIFFRACTION96.6
3.87-4.170.23811490.18623646X-RAY DIFFRACTION96.05
4.17-4.590.1881350.15273571X-RAY DIFFRACTION94.69
4.59-5.250.20491420.14193669X-RAY DIFFRACTION97.05
5.25-6.620.19271270.17713467X-RAY DIFFRACTION91.85
6.62-47.990.22731410.1673719X-RAY DIFFRACTION97.52

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