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- PDB-6z7w: Human insulin in complex with the analytical antibody HUI-018 Fab -

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Basic information

Entry
Database: PDB / ID: 6z7w
TitleHuman insulin in complex with the analytical antibody HUI-018 Fab
Components
  • (Insulin) x 2
  • HUI-018 Fab Heavy Chain
  • MAb 6H10 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 feeding behavior / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / 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 feeding behavior / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / 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 / negative regulation of protein secretion / activation of protein kinase B activity / 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 / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / transport vesicle / nitric oxide-cGMP-mediated signaling / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / endosome lumen / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / 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 / Amyloid fiber formation / endoplasmic reticulum lumen / 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: 2.42 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAb 6H10 light chain
B: HUI-018 Fab Heavy Chain
C: MAb 6H10 light chain
D: HUI-018 Fab Heavy Chain
E: MAb 6H10 light chain
F: HUI-018 Fab Heavy Chain
G: MAb 6H10 light chain
H: HUI-018 Fab Heavy Chain
I: Insulin
J: Insulin
K: Insulin
L: Insulin
M: Insulin
N: Insulin
O: Insulin
P: Insulin


Theoretical massNumber of molelcules
Total (without water)213,39416
Polymers213,39416
Non-polymers00
Water12,845713
1
A: MAb 6H10 light chain
B: HUI-018 Fab Heavy Chain
I: Insulin
J: Insulin


Theoretical massNumber of molelcules
Total (without water)53,3494
Polymers53,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MAb 6H10 light chain
B: HUI-018 Fab Heavy Chain
G: MAb 6H10 light chain
H: HUI-018 Fab Heavy Chain
I: Insulin
J: Insulin
O: Insulin
P: Insulin


Theoretical massNumber of molelcules
Total (without water)106,6978
Polymers106,6978
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MAb 6H10 light chain
D: HUI-018 Fab Heavy Chain
K: Insulin
L: Insulin


Theoretical massNumber of molelcules
Total (without water)53,3494
Polymers53,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: MAb 6H10 light chain
D: HUI-018 Fab Heavy Chain
E: MAb 6H10 light chain
F: HUI-018 Fab Heavy Chain
K: Insulin
L: Insulin
M: Insulin
N: Insulin


Theoretical massNumber of molelcules
Total (without water)106,6978
Polymers106,6978
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: MAb 6H10 light chain
F: HUI-018 Fab Heavy Chain
M: Insulin
N: Insulin


Theoretical massNumber of molelcules
Total (without water)53,3494
Polymers53,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
G: MAb 6H10 light chain
H: HUI-018 Fab Heavy Chain
O: Insulin
P: Insulin


Theoretical massNumber of molelcules
Total (without water)53,3494
Polymers53,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.230, 216.610, 101.090
Angle α, β, γ (deg.)90.000, 103.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 213)
d_2ens_1chain "C"
d_3ens_1(chain "E" and resid 1 through 213)
d_4ens_1(chain "G" and resid 1 through 213)
d_1ens_2(chain "B" and (resid 1 through 130 or resid 138 through 216))
d_2ens_2chain "D"
d_3ens_2(chain "F" and resid 1 through 216)
d_4ens_2(chain "H" and (resid 1 through 130 or resid 138 through 216))
d_1ens_3chain "J"
d_2ens_3chain "L"
d_3ens_3(chain "N" and resid 5 through 28)
d_4ens_3(chain "P" and resid 5 through 28)
d_1ens_4chain "K"
d_2ens_4chain "M"
d_3ens_4chain "O"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPGLUA1 - 213
d_21ens_1ASPGLUC1 - 213
d_31ens_1ASPGLUE1 - 213
d_41ens_1ASPGLUG1 - 213
d_11ens_2GLNPROB1 - 134
d_12ens_2SERPROB138 - 216
d_21ens_2GLNPROD1 - 213
d_31ens_2GLNPROF1 - 213
d_41ens_2GLNPROH1 - 134
d_42ens_2SERPROH138 - 216
d_11ens_3HISPROJ1 - 24
d_21ens_3HISPROL1 - 24
d_31ens_3HISPRON1 - 24
d_41ens_3HISPROP2 - 25
d_11ens_4GLYASNK1 - 21
d_21ens_4GLYASNM1 - 21
d_31ens_4GLYASNO1 - 21

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

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Components

#1: Antibody
MAb 6H10 light chain


Mass: 23809.334 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: LC / Production host: Homo sapiens (human)
#2: Antibody
HUI-018 Fab Heavy Chain


Mass: 23721.527 Da / Num. of mol.: 4
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.: 4
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.: 4
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.: 713 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Hepes, pH 7, 20 % (v/w) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→29.9 Å / Num. obs: 77030 / % possible obs: 96.78 % / Redundancy: 2.8 % / Biso Wilson estimate: 34.51 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.07496 / Rrim(I) all: 0.1313 / Net I/σ(I): 9.06
Reflection shellResolution: 2.42→2.597 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.7945 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 17424 / CC1/2: 0.565 / CC star: 0.85 / Rpim(I) all: 0.6057 / Rrim(I) all: 1.004 / % possible all: 90.97

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1200000000 / Resolution: 2.42→29.87 Å / SU ML: 0.4385 / Cross valid method: FREE R-VALUE / σ(F): 0.92 / Phase error: 31.9015
RfactorNum. reflection% reflection
Rfree0.2746 3581 2.53 %
Rwork0.2093 --
obs0.2109 77014 89.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.78 Å2
Refinement stepCycle: LAST / Resolution: 2.42→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14579 0 0 713 15292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009814911
X-RAY DIFFRACTIONf_angle_d1.346620300
X-RAY DIFFRACTIONf_chiral_restr0.06582315
X-RAY DIFFRACTIONf_plane_restr0.00912590
X-RAY DIFFRACTIONf_dihedral_angle_d20.22395299
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.78453811597
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.95904421613
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.778384878914
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.876134102385
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS1.0809613821
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.856144309232
ens_3d_2JX-RAY DIFFRACTIONTorsion NCS1.63170219855
ens_3d_3JX-RAY DIFFRACTIONTorsion NCS1.47540600251
ens_3d_4JX-RAY DIFFRACTIONTorsion NCS1.66656843668
ens_4d_2KX-RAY DIFFRACTIONTorsion NCS1.06282542696
ens_4d_3KX-RAY DIFFRACTIONTorsion NCS1.15016509493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.450.41000.36033870X-RAY DIFFRACTION66.94
2.45-2.480.41771220.35125228X-RAY DIFFRACTION86.89
2.48-2.520.42781420.32855293X-RAY DIFFRACTION87.89
2.52-2.560.4021320.31685168X-RAY DIFFRACTION89.36
2.56-2.60.37941480.32065374X-RAY DIFFRACTION89.7
2.6-2.640.35271340.30345387X-RAY DIFFRACTION90.17
2.64-2.680.36911400.29925295X-RAY DIFFRACTION90.03
2.68-2.730.34821300.29095317X-RAY DIFFRACTION89.84
2.73-2.790.34751390.27735465X-RAY DIFFRACTION91.46
2.79-2.840.35591420.28485324X-RAY DIFFRACTION91.33
2.84-2.90.42991540.27125394X-RAY DIFFRACTION91.04
2.9-2.970.37461510.25075491X-RAY DIFFRACTION92.16
2.97-3.050.27511370.23715314X-RAY DIFFRACTION90.97
3.05-3.130.27881400.22315565X-RAY DIFFRACTION92.55
3.13-3.220.31581440.21425382X-RAY DIFFRACTION91.84
3.22-3.320.27561430.21585508X-RAY DIFFRACTION91.78
3.32-3.440.30341350.2035424X-RAY DIFFRACTION92.42
3.44-3.580.27661530.18945484X-RAY DIFFRACTION91.7
3.58-3.740.22811350.185414X-RAY DIFFRACTION92.01
3.74-3.940.26431370.17145428X-RAY DIFFRACTION91.86
3.94-4.190.22761370.15955487X-RAY DIFFRACTION91.45
4.19-4.510.17391300.14255294X-RAY DIFFRACTION90.04
4.51-4.960.2011390.14245336X-RAY DIFFRACTION89.7
4.96-5.670.20781460.15815377X-RAY DIFFRACTION90.79
5.67-7.130.24641430.1895346X-RAY DIFFRACTION90.49
7.13-29.870.18181280.17425275X-RAY DIFFRACTION89

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