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- PDB-7jp3: Des-B29,B30-insulin -

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Basic information

Entry
Database: PDB / ID: 7jp3
TitleDes-B29,B30-insulin
ComponentsInsulin B chain,Insulin A chain
KeywordsHORMONE / insulin mutant / stability
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYoder, J. / Weiss, M.A. / DiMarchi, R. / Zaykov, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK409049 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK118536 United States
CitationJournal: To Be Published
Title: Des-B29,B30-insulin
Authors: Yoder, J. / Weiss, M.A.
History
DepositionAug 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin B chain,Insulin A chain
B: Insulin B chain,Insulin A chain
C: Insulin B chain,Insulin A chain
D: Insulin B chain,Insulin A chain
E: Insulin B chain,Insulin A chain
F: Insulin B chain,Insulin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,37516
Polymers33,6096
Non-polymers76610
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.606, 60.001, 61.448
Angle α, β, γ (deg.)90.000, 95.170, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

21C-211-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 1 - 49 / Label seq-ID: 1 - 49

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF

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Components

#1: Protein/peptide
Insulin B chain,Insulin A chain


Mass: 5601.417 Da / Num. of mol.: 6
Mutation: Residues corresponding to B chain amino acids 29-30 were deleted, and Pro-28 was mutated to Lys. This, in effect, is the equivalent of deleting only residues 28 and 30 of the wild-type B chain.
Source method: obtained synthetically
Details: This is a fusion protein consisting of a mutant insulin B chain followed by the insulin A chain. Six of these fusion chains are in the asymmetric unit
Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Chemical
ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThis construct contains a mutant of the naturally occurring insulin B chain and the wild-type ...This construct contains a mutant of the naturally occurring insulin B chain and the wild-type naturally occurring A chain fused together into one peptide chain.

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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: 1.96 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1:2.5 ratio of Zn2+ to protein monomer in 0.02M Tris-HCl, 0.05M sodium citrate, 5% acetone, 0.03% phenol, 0.01% zinc acetate, PH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.949→50 Å / Num. obs: 18729 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.038 / Rrim(I) all: 0.074 / Χ2: 1.154 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.983.70.7319130.6090.440.8550.75698.3
1.98-2.023.80.6079150.7180.360.7060.76397.9
2.02-2.063.80.5389300.7290.320.6270.76698.2
2.06-2.13.80.4579220.8380.2710.5320.81298.3
2.1-2.153.80.3319330.8980.1960.3850.88298.2
2.15-2.23.80.2949310.9130.1740.3420.90298.6
2.2-2.253.80.2479380.9330.1470.2880.96898.6
2.25-2.313.80.2259230.950.1330.2620.93798.4
2.31-2.383.80.1839170.9590.1080.2120.94798.8
2.38-2.463.80.1759530.9680.1040.2041.04198.8
2.46-2.543.80.1428980.9760.0840.1651.07398.8
2.54-2.653.80.1159460.9820.0690.1341.07899
2.65-2.773.80.0999580.9860.0590.1161.20599.2
2.77-2.913.80.0839360.990.050.0961.29399.2
2.91-3.13.80.0719340.9930.0420.0821.36399.3
3.1-3.333.70.0629570.9930.0370.0721.65799.5
3.33-3.673.70.059240.9960.030.0581.6899.6
3.67-4.23.60.049630.9970.0240.0471.65799.8
4.2-5.293.70.0349590.9970.0210.041.45999.4
5.29-503.60.0379790.9970.0230.0431.8699.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XW7

1xw7


Resolution: 1.95→37.8 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 925 4.94 %
Rwork0.2137 17800 -
obs0.2155 18725 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.27 Å2 / Biso mean: 41.0947 Å2 / Biso min: 20.19 Å2
Refinement stepCycle: final / Resolution: 1.95→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 46 77 2463
Biso mean--33.6 48 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092448
X-RAY DIFFRACTIONf_angle_d1.3823276
X-RAY DIFFRACTIONf_chiral_restr0.068354
X-RAY DIFFRACTIONf_plane_restr0.007420
X-RAY DIFFRACTIONf_dihedral_angle_d14.424828
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1342X-RAY DIFFRACTION21.596TORSIONAL
12B1342X-RAY DIFFRACTION21.596TORSIONAL
13C1342X-RAY DIFFRACTION21.596TORSIONAL
14D1342X-RAY DIFFRACTION21.596TORSIONAL
15E1342X-RAY DIFFRACTION21.596TORSIONAL
16F1342X-RAY DIFFRACTION21.596TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.05150.30091350.2571240795
2.0515-2.180.30561380.2323250198
2.18-2.34830.2661170.2168257599
2.3483-2.58460.29771320.2168255399
2.5846-2.95850.24151290.2134255099
2.9585-3.72680.25021330.2195259799
3.7268-37.7940.22451410.2021261799

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