[English] 日本語
Yorodumi
- PDB-5uru: Insulin with proline analog DhP at position B28 in the R6 state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uru
TitleInsulin with proline analog DhP at position B28 in the R6 state
Components(Insulin Chain ...) x 2
KeywordsHORMONE / Insulin Hormone
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / IRS activation / negative regulation of NAD(P)H oxidase activity / Insulin processing / Insulin receptor recycling / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / IRS activation / negative regulation of NAD(P)H oxidase activity / Insulin processing / Insulin receptor recycling / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / alpha-beta T cell activation / negative regulation of gluconeogenesis / negative regulation of acute inflammatory response / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of dendritic spine maintenance / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of glycogen biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of protein secretion / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of lipid biosynthetic process / Signal attenuation / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / positive regulation of insulin receptor signaling pathway / Regulation of insulin secretion / endoplasmic reticulum-Golgi intermediate compartment membrane / transport vesicle / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of protein metabolic process / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of brown fat cell differentiation / positive regulation of mitotic nuclear division / positive regulation of long-term synaptic potentiation / regulation of transmembrane transporter activity / positive regulation of cell differentiation / regulation of synaptic plasticity / activation of protein kinase B activity / cognition / positive regulation of cytokine production / positive regulation of protein secretion / acute-phase response / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of nitric-oxide synthase activity / hormone activity / insulin receptor binding / vasodilation / insulin receptor signaling pathway / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / wound healing / Golgi lumen / regulation of protein localization / glucose metabolic process / glucose homeostasis / cell-cell signaling / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / positive regulation of NF-kappaB transcription factor activity / positive regulation of protein kinase B signaling / positive regulation of MAPK cascade / protease binding / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / endoplasmic reticulum lumen / 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-like / Insulin / insulin-like growth factor / relaxin family. / Insulin family signature. / Insulin, conserved site / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.41 Å
AuthorsLieblich, S.A. / Fang, K.Y. / Tirrell, D.A.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: To Be Published
Title: Insulin with proline analog DhP at position B28 in the R6 state
Authors: Lieblich, S.A. / Fang, K.Y. / Tirrell, D.A.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin Chain A
B: Insulin Chain B
C: Insulin Chain A
D: Insulin Chain B
E: Insulin Chain A
F: Insulin Chain B
G: Insulin Chain A
H: Insulin Chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,04220
Polymers23,2638
Non-polymers78012
Water1086
1
A: Insulin Chain A
B: Insulin Chain B
C: Insulin Chain A
D: Insulin Chain B
hetero molecules

A: Insulin Chain A
B: Insulin Chain B
C: Insulin Chain A
D: Insulin Chain B
hetero molecules

A: Insulin Chain A
B: Insulin Chain B
C: Insulin Chain A
D: Insulin Chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,06430
Polymers34,89412
Non-polymers1,17018
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area19320 Å2
ΔGint-473.2 kcal/mol
Surface area10730 Å2
MethodPISA
2
E: Insulin Chain A
F: Insulin Chain B
G: Insulin Chain A
H: Insulin Chain B
hetero molecules

E: Insulin Chain A
F: Insulin Chain B
G: Insulin Chain A
H: Insulin Chain B
hetero molecules

E: Insulin Chain A
F: Insulin Chain B
G: Insulin Chain A
H: Insulin Chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,06430
Polymers34,89412
Non-polymers1,17018
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area20300 Å2
ΔGint-727.4 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.259, 79.259, 79.874
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-101-

ZN

21B-102-

CL

31D-101-

ZN

41D-102-

CL

51F-101-

ZN

61F-102-

CL

71H-101-

ZN

81H-102-

CL

91F-201-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 21
2111C1 - 21
1121A1 - 21
2121E1 - 21
1131A1 - 21
2131G1 - 21
1141B2 - 27
2141D2 - 27
1151B2 - 27
2151F2 - 27
1161B1 - 28
2161H1 - 28
1171C1 - 21
2171E1 - 21
1181C1 - 21
2181G1 - 21
1191D2 - 28
2191F2 - 28
11101D2 - 27
21101H2 - 27
11111E1 - 21
21111G1 - 21
11121F2 - 27
21121H2 - 27

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

NCS oper:
IDCodeMatrixVector
1given(1, 1), (1, 1), (1)1
2given(2, 0.905032, 0.422339), (2, 0.423438, -0.905831), (2, 0.040225, 0.033159)0.050477, -0.013021, -0.99864
3given(1, 1), (1, 1), (1)1
4given(2, 0.996365, 0.081633), (2, -0.08136, 0.996613), (2, 0.025232, -0.009966)-0.024336, 0.011989, 0.999632
5given(1, 1), (1, 1), (1)1
6given(2, 0.870404, 0.490494), (2, 0.491373, -0.870855), (2, 0.030796, 0.032052)0.042569, -0.012793, -0.999012
7given(1, 1), (1, 1), (1)1
8given(2, 0.864889, 0.501028), (2, 0.501105, -0.865368), (2, -0.029332, -0.010464)-0.030627, -0.005646, -0.999515
9given(1, 1), (1, 1), (1)1
10given(2, 0.996011, 0.089172), (2, -0.089183, 0.99601), (2, -0.003, -0.003661)0.003315, 0.003379, 0.999989
11given(1, 1), (1, 1), (1)1
12given(2, 0.807434, 0.589305), (2, 0.58963, -0.80766), (2, -0.019665, -0.020103)-0.027736, 0.004643, -0.999605
13given(1, 1), (1, 1), (1)1
14given(2, 0.868059, 0.495886), (2, 0.495728, -0.868387), (2, 0.026981, 0.000926)0.023889, 0.012575, -0.999636
15given(1, 1), (1, 1), (1)1
16given(2, 0.997444, 0.070969), (2, -0.070976, 0.997478), (2, 0.008268, 0.00124)-0.008335, -0.00065, 0.999965
17given(1, 1), (1, 1), (1)1
18given(2, 0.818119, 0.574538), (2, 0.574521, -0.818447), (2, -0.02466, -0.007092)-0.024257, -0.008366, -0.999671
19given(1, 1), (1, 1), (1)1
20given(2, 0.994282, 0.106581), (2, -0.106494, 0.994237), (2, -0.00789, 0.011575)0.006611, -0.012349, 0.999902
21given(1, 1), (1, 1), (1)1
22given(2, 0.829059, 0.558836), (2, 0.558914, -0.829224), (2, 0.016617, 0.009444)0.019058, 0.001456, -0.999817
23given(1, 1), (1, 1), (1)1
24given(2, 0.75009, 0.660746), (2, 0.661164, -0.750189), (2, -0.015083, -0.025129)-0.02793, 0.008884, -0.99957

-
Components

-
Insulin Chain ... , 2 types, 8 molecules ACEGBDFH

#1: Protein/peptide
Insulin Chain A


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: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide
Insulin Chain B


Mass: 3431.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308

-
Non-polymers , 4 types, 18 molecules

#3: Chemical
ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 300mM Tris pH 8, 17mM Zinc Acetate, 1% Phenol, 313mM Sodium Citrate, 11.25% Acetone
Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2016
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.68→52.06 Å / Num. obs: 18094 / % possible obs: 84.1 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.042 / Rrim(I) all: 0.097 / Net I/σ(I): 5.4 / Num. measured all: 82670 / Scaling rejects: 51
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) all% possible allCC1/2Net I/σ(I) obs
1.68-1.711.11.2654511.261.7824.5
9.02-34.525.80.0437981370.020.04798.30.99822.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.17 Å34.52 Å
Translation4.17 Å34.52 Å

-
Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.3.11data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EV6
Resolution: 2.41→52.06 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.2003 / FOM work R set: 0.785 / SU B: 20.717 / SU ML: 0.225 / SU R Cruickshank DPI: 0.5636 / SU Rfree: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.564 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 376 5.2 %RANDOM
Rwork0.1868 ---
obs0.1902 6816 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.57 Å2 / Biso mean: 56.008 Å2 / Biso min: 18.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 2.41→52.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1420 0 36 6 1462
Biso mean--47.87 52.7 -
Num. residues----194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191486
X-RAY DIFFRACTIONr_bond_other_d0.0020.021258
X-RAY DIFFRACTIONr_angle_refined_deg2.0351.9672016
X-RAY DIFFRACTIONr_angle_other_deg1.19832874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0335186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.12723.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63415194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.89153
X-RAY DIFFRACTIONr_chiral_restr0.1120.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021653
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02334
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A189TIGHT POSITIONAL0.090.09
1A139TIGHT POSITIONAL0.130.09
1A186TIGHT POSITIONAL0.320.09
1A151TIGHT THERMAL3.480.87
2A139TIGHT THERMAL2.920.87
3A151TIGHT THERMAL2.90.87
4B192TIGHT THERMAL3.120.87
5B192TIGHT THERMAL4.640.87
6B198TIGHT THERMAL2.720.87
7C139TIGHT THERMAL3.010.87
8C158TIGHT THERMAL2.910.87
9D199TIGHT THERMAL2.550.87
10D189TIGHT THERMAL2.110.87
11E139TIGHT THERMAL3.680.87
12F186TIGHT THERMAL2.970.87
LS refinement shellResolution: 2.41→2.472 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 26 -
Rwork0.225 469 -
all-495 -
obs--99.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.47191.7314.3395.95370.65829.36180.0374-0.3162-0.40580.1727-0.0963-0.03950.5964-0.53510.05880.0803-0.05940.03290.08880.04380.21-10.961533.823611.7201
25.11511.0225-0.83364.80820.76732.9980.1034-0.0805-0.39380.07390.1690.31390.0981-0.4939-0.27240.0073-0.0244-0.01050.14350.04820.2725-10.198340.61236.6442
34.61380.4841-1.73426.9363-0.8056.06510.1110.85610.2406-0.4456-0.11080.5268-0.1595-0.6016-0.00020.10490.0594-0.14230.39150.11490.3049-15.043352.3072-6.1254
45.5564-0.9143-2.73416.3242-0.52493.9686-0.15970.5389-0.1143-0.47390.12370.74060.1394-0.55450.0360.0522-0.0248-0.08210.1613-0.01350.1898-11.4945.6445-0.9717
56.9476-4.12911.88357.1769-2.417711.79170.2863-0.6445-0.65530.7411-0.30470.17520.7532-0.11190.01840.3099-0.13450.03440.19020.16390.2619-10.076932.8374-28.6969
66.57751.89541.22515.17080.97063.17940.1274-0.4448-0.48460.455-0.01680.31860.3633-0.2012-0.11060.0855-0.03740.04250.09330.04510.1442-9.649339.4162-33.6134
75.3255-2.1434-4.53817.7337-2.2346.53810.01160.46990.0746-0.19940.11150.46810.0343-0.6769-0.12310.030.0476-0.05530.23640.04340.3113-15.598650.3558-46.2305
84.3628-1.2989-1.25213.86581.89324.95820.03760.1780.099-0.11510.20410.42890.2317-0.5565-0.24170.0286-0.0582-0.02060.13460.06540.2295-10.888243.8989-41.8519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2B1 - 27
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION4D2 - 27
5X-RAY DIFFRACTION5E1 - 21
6X-RAY DIFFRACTION6F2 - 27
7X-RAY DIFFRACTION7G1 - 21
8X-RAY DIFFRACTION8H1 - 27

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more