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- PDB-6z7y: Human insulin in complex with the analytical antibody OXI-005 Fab -

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Basic information

Entry
Database: PDB / ID: 6z7y
TitleHuman 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


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 / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...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 / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / 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 / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of cytokine production / positive regulation of glycolytic process / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / Regulation of insulin secretion / positive regulation of cell differentiation / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / Golgi lumen / positive regulation of protein localization to nucleus / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / 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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)106,2298
Polymers106,2298
Non-polymers00
Water5,981332
1
A: OXI-005 Fab Light chain
B: OXI-005 Fab Heavy chain
G: Insulin
H: Insulin


Theoretical massNumber of molelcules
Total (without water)53,1144
Polymers53,1144
Non-polymers00
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


Theoretical massNumber of molelcules
Total (without water)53,1144
Polymers53,1144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.390, 173.230, 83.800
Angle α, β, γ (deg.)90.000, 135.829, 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
111ASPASPASNASN(chain 'A' and resid 1 through 211)AA1 - 2111 - 211
221ASPASPASNASNchain 'C'CC1 - 2111 - 211
132GLUGLUPROPRO(chain 'B' and (resid 1 through 130 or resid 138 through 143 or resid 145 through 216))BB1 - 1301 - 130
142SERSERLEULEU(chain 'B' and (resid 1 through 130 or resid 138 through 143 or resid 145 through 216))BB138 - 142138 - 142
152LEULEUPROPRO(chain 'B' and (resid 1 through 130 or resid 138 through 143 or resid 145 through 216))BB145 - 216145 - 216
262GLUGLUPROPRO(chain 'D' and (resid 1 through 143 or resid 145 through 216))DD1 - 1301 - 130
272SERSERLEULEU(chain 'D' and (resid 1 through 143 or resid 145 through 216))DD138 - 142138 - 142
282LEULEUPROPRO(chain 'D' and (resid 1 through 143 or resid 145 through 216))DD145 - 216145 - 216
193GLYGLYASNASNchain 'E'EE1 - 211 - 21
2103GLYGLYASNASNchain 'G'GG1 - 211 - 21
1114ASNASNTHRTHR(chain 'F' and resid 3 through 30)FF3 - 303 - 30
2124ASNASNTHRTHRchain 'H'HH3 - 303 - 30

NCS ensembles :
ID
1
2
3
4

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Components

#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)
#3: Protein/peptide Insulin


Mass: 2383.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#4: Protein/peptide Insulin


Mass: 3433.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M magnesium chloride, 0.1 M Tris, pH 8, 20 % (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.42 Å / Num. obs: 54923 / % possible obs: 99.02 % / Redundancy: 3.4 % / Biso Wilson estimate: 46.01 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.09194 / Rpim(I) all: 0.05942 / Rrim(I) all: 0.1098 / Net I/σ(I): 8.88
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.8584 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 19188 / CC1/2: 0.549 / CC star: 0.842 / Rpim(I) all: 0.5396 / Rrim(I) all: 1.016 / % possible all: 99.59

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Processing

Software
NameVersionClassification
PHENIXdev_3714refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z7X

6z7x


Resolution: 2.2→48.42 Å / SU ML: 0.3889 / Cross valid method: FREE R-VALUE / σ(F): 0.91 / Phase error: 32.7635
RfactorNum. reflection% reflection
Rfree0.2526 3818 3.69 %
Rwork0.2168 --
obs0.2182 54914 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7286 0 0 332 7618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00957476
X-RAY DIFFRACTIONf_angle_d1.273410175
X-RAY DIFFRACTIONf_chiral_restr0.06331140
X-RAY DIFFRACTIONf_plane_restr0.00751295
X-RAY DIFFRACTIONf_dihedral_angle_d20.03822680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.44391540.37613782X-RAY DIFFRACTION95.98
2.23-2.260.41321470.36713767X-RAY DIFFRACTION96.19
2.26-2.290.33171330.35573692X-RAY DIFFRACTION95.39
2.29-2.320.39871310.35053763X-RAY DIFFRACTION95.46
2.32-2.360.39571510.3513667X-RAY DIFFRACTION95.07
2.36-2.390.35291490.32473813X-RAY DIFFRACTION94.45
2.39-2.430.38531240.33063691X-RAY DIFFRACTION94.52
2.43-2.470.38381530.32593626X-RAY DIFFRACTION93.75
2.47-2.520.35671550.32233654X-RAY DIFFRACTION94.28
2.52-2.570.33211530.32113772X-RAY DIFFRACTION94.72
2.57-2.620.40881160.28863761X-RAY DIFFRACTION95.82
2.62-2.680.32441620.28523760X-RAY DIFFRACTION96.58
2.68-2.740.33121490.27243749X-RAY DIFFRACTION96.53
2.74-2.810.30081150.24953807X-RAY DIFFRACTION96.25
2.81-2.880.27391330.24063831X-RAY DIFFRACTION97.06
2.88-2.970.27821670.22563756X-RAY DIFFRACTION95.96
2.97-3.060.29321300.2333752X-RAY DIFFRACTION95.83
3.06-3.170.27061430.2323740X-RAY DIFFRACTION94.66
3.17-3.30.33861560.22873552X-RAY DIFFRACTION92.45
3.3-3.450.2471260.21983721X-RAY DIFFRACTION93.42
3.45-3.630.21121360.20473620X-RAY DIFFRACTION92.54
3.63-3.860.25621380.19663617X-RAY DIFFRACTION93.08
3.86-4.160.18771430.17313546X-RAY DIFFRACTION90.75
4.16-4.570.16281350.15073524X-RAY DIFFRACTION89.48
4.58-5.240.17051360.14383540X-RAY DIFFRACTION90.34
5.24-6.590.19541350.17913603X-RAY DIFFRACTION91.96
6.6-48.420.21341480.1723656X-RAY DIFFRACTION93.08

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