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Basic information

Entry
Database: PDB / ID: 1rwe
TitleEnhancing the activity of insulin at receptor edge: crystal structure and photo-cross-linking of A8 analogues
Components
  • Insulin
  • insulin
KeywordsHORMONE/GROWTH FACTOR / A8-Histidine human insulin / insulin receptor / HORMONE-GROWTH FACTOR COMPLEX
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 / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / 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 glycolytic process / positive regulation of cytokine production / 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 / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWan, Z. / Xu, B. / Chu, Y.C. / Li, B. / Nakagawa, S.H. / Qu, Y. / Hu, S.Q. / Katsoyannis, P.G. / Weiss, M.A.
Citation
Journal: Biochemistry / Year: 2004
Title: Enhancing the activity of insulin at the receptor interface: crystal structure and photo-cross-linking of A8 analogues.
Authors: Wan, Z. / Xu, B. / Huang, K. / Chu, Y.C. / Li, B. / Nakagawa, S.H. / Qu, Y. / Hu, S.Q. / Katsoyannis, P.G. / Weiss, M.A.
#1: Journal: Biochemistry / Year: 1995
Title: X-ray crystallographic studies on hexameric insulins in the presence of helix-stabilizing agents,thiocyanate, methylparahben, and phenol
Authors: Whittingham, J.L. / Chaudhuri, S. / Dodson, E.J. / Moody, P.C. / Dodson, G.G.
#2: Journal: Structure / Year: 1995
Title: Role of c-terminal B-chain residues in insulin assemble: the structure of hexameric LysB28ProB29-human insulin
Authors: Ciszak, E. / Beals, J.M. / Frank, B.H. / Baker, J.C. / Carter, D.C. / Smith, G.D.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Phase changes in T3R3f human insulin: temperature or pressure insulin
Authors: Smith, G.D. / Blessing, R.H.
#4: Journal: J.Mol.Biol. / Year: 2002
Title: Non-standard insulin design:structure-activity relationship at the periphery of the insulin receptor
Authors: Weiss, M.A. / Wan, Z.L. / Zhao, M. / Chu, Y.C. / Nakagawa, S.H. / Burke, G.T. / Jia, W.H. / Hellmich, R. / Katsoyannis, P.G.
#5: Journal: Biochemistry / Year: 2003
Title: Crystal structure of allo-IleA2-insulin, an , an inactive chiral analogue: implications for the mechanism of receptor binding
Authors: Wan, Z.L. / Xu, B. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A.
History
DepositionDec 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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: insulin
B: Insulin
C: insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0059
Polymers11,7094
Non-polymers2965
Water2,450136
1
A: insulin
B: Insulin
hetero molecules

A: insulin
B: Insulin
hetero molecules

A: insulin
B: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,86712
Polymers17,5646
Non-polymers3036
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5370 Å2
ΔGint-124 kcal/mol
Surface area10920 Å2
MethodPISA
2
C: insulin
D: Insulin
hetero molecules

C: insulin
D: Insulin
hetero molecules

C: insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,14915
Polymers17,5646
Non-polymers5859
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5960 Å2
ΔGint-157 kcal/mol
Surface area10020 Å2
MethodPISA
3
A: insulin
B: Insulin
C: insulin
D: Insulin
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)36,01627
Polymers35,12812
Non-polymers88815
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area19030 Å2
ΔGint-319 kcal/mol
Surface area13230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.341, 79.341, 34.708
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-201-

ZN

21B-202-

CL

31D-301-

ZN

41D-302-

CL

51D-303-

HOH

61D-304-

HOH

DetailsThe biological assembly is hexamer generated from the dimer in the asymmetric unit by the operations: -y,x-y,z and -x+y,-x,z The crystallographic asymmetric unit of insulin consists of two insulin monomers each consisting of two heterochains The entry present coordinates for monomer 1 (chain indicators A and B) and monomer2 (chain indicators C and D) There are two zinc ions per insulin hexamer located on the three-fold axis The conformations of two monomers are different as the result of B change in conformation of first eight residues of the B-chain

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide insulin


Mass: 2420.741 Da / Num. of mol.: 2 / Fragment: insulin A chain / Mutation: T8H / Source method: obtained synthetically / Keywords: T8H / References: UniProt: P01308
#2: Protein/peptide Insulin


Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: insulin B chain / Source method: obtained synthetically / References: UniProt: P01308

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Non-polymers , 4 types, 141 molecules

#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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.8 Å3/Da / Density % sol: 31.49 %
Crystal growTemperature: 298 K / pH: 6.8
Details: Tris, sodium citrate, acetone, phenol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.978
DetectorType: ADSC / Detector: CCD / Date: Aug 19, 1998
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→19.18 Å / Num. obs: 7426 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 23.52
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 9.2 / % possible all: 95.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1TRZ AND 1MPJ

1trz

1mpj


Resolution: 1.8→19.18 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.245 796 10.7 %RANDOM
Rwork0.189 ---
obs0.189 7426 98.4 %-
all-7523 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1019 Å2 / ksol: 0.336481 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å2-0.29 Å20 Å2
2---1.61 Å20 Å2
3---3.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.02 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 11 136 963
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.132.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 120 10 %
Rwork0.202 --
obs--95.4 %

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