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- PDB-1g7b: 1.3 A STRUCTURE OF T3R3 HUMAN INSULIN AT 100 K -

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Basic information

Entry
Database: PDB / ID: 1g7b
Title1.3 A STRUCTURE OF T3R3 HUMAN INSULIN AT 100 K
Components
  • INSULIN A-CHAIN
  • INSULIN B-CHAIN
Keywordshormone/growth factor / T3R3 Human Insulin Hexamer / hormone-growth factor COMPLEX
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 / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSmith, G.D. / Pangborn, W.A. / Blessing, R.H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Phase changes in T(3)R(3)(f) human insulin: temperature or pressure induced?
Authors: Smith, G.D. / Pangborn, W.A. / Blessing, R.H.
#1: Journal: Biochemistry / Year: 1995
Title: X-ray Crystallographic Studies on Hexameric Insulins in the Presence of Helix-Stabilizing Agents, Thiocyanate, Methylparaben, and Phenol
Authors: Whittingham, J.L. / Chaudhuri, S. / Dodson, E.J. / Moody, P.C.E. / Dodson, G.G.
#2: Journal: Biochemistry / Year: 1994
Title: Crystallographic Evidence for Dual Coordination around Zinc in the T3R3 Human Insulin Hexamer
Authors: Ciszak, E. / Smith, G.D.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984
Title: Structural stability in the 4-zinc human insulin hexamer
Authors: Smith, G.D. / Swenson, D.C. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D.
#4: Journal: Nature / Year: 1976
Title: Structure of 4-zinc insulin
Authors: Bentley, G. / Dodson, E. / Dodson, G.G. / Hodgkin, D. / Mercola, D.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The First Protein Crystal Structure Determined from High Resolution X-Ray Powder Diffraction Data: A Variant of T3R3 Human Insulin Zinc Complex Produced by Grinding
Authors: Von Dreele, R.B. / Stephens, P.W. / Smith, G.D. / Blessing, R.H.
History
DepositionNov 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INSULIN A-CHAIN
B: INSULIN B-CHAIN
C: INSULIN A-CHAIN
D: INSULIN B-CHAIN
E: INSULIN A-CHAIN
F: INSULIN B-CHAIN
G: INSULIN A-CHAIN
H: INSULIN B-CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,12724
Polymers23,2718
Non-polymers85616
Water3,819212
1
A: INSULIN A-CHAIN
B: INSULIN B-CHAIN
C: INSULIN A-CHAIN
D: INSULIN B-CHAIN
hetero molecules

A: INSULIN A-CHAIN
B: INSULIN B-CHAIN
C: INSULIN A-CHAIN
D: INSULIN B-CHAIN
hetero molecules

A: INSULIN A-CHAIN
B: INSULIN B-CHAIN
C: INSULIN A-CHAIN
D: INSULIN B-CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,31239
Polymers34,90612
Non-polymers1,40727
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
E: INSULIN A-CHAIN
F: INSULIN B-CHAIN
G: INSULIN A-CHAIN
H: INSULIN B-CHAIN
hetero molecules

E: INSULIN A-CHAIN
F: INSULIN B-CHAIN
G: INSULIN A-CHAIN
H: INSULIN B-CHAIN
hetero molecules

E: INSULIN A-CHAIN
F: INSULIN B-CHAIN
G: INSULIN A-CHAIN
H: INSULIN B-CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,06833
Polymers34,90612
Non-polymers1,16221
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)80.050, 80.050, 71.459
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingrhombohedral
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-901-

ZN

21B-902-

CL

31D-911-

ZN

41D-912-

CL

51F-931-

ZN

61F-932-

CL

71H-941-

ZN

81H-942-

CL

91B-1214-

HOH

101D-1150-

HOH

111D-1814-

HOH

121D-1950-

HOH

131F-1181-

HOH

141F-1870-

HOH

DetailsThe second dimer of the T3R3 insulin hexamer is generated by the crystallographic three-fold axis: -y, x-y, z / The third dimer of the T3R3 insulin hexamer is generated by the crystallographic three-fold axis: y-x, -x, z

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Components

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Protein/peptide , 2 types, 8 molecules ACEGBDFH

#1: Protein/peptide
INSULIN A-CHAIN


Mass: 2383.698 Da / Num. of mol.: 4 / Fragment: A-CHAIN / Source method: obtained synthetically
Details: This sequence occurs naturally in homo sapiens (Human)
References: UniProt: P01308
#2: Protein/peptide
INSULIN B-CHAIN


Mass: 3433.953 Da / Num. of mol.: 4 / Fragment: B-CHAIN / Source method: obtained synthetically
Details: This sequence occurs naturally in homo sapiens (Human)
References: UniProt: P01308

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Non-polymers , 5 types, 228 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACN / ACETONE / Acetone


Mass: 58.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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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: 1.89 Å3/Da / Density % sol: 35.03 %
Crystal growTemperature: 298 K / Method: slow cooling / pH: 6.3
Details: 5 mg/ml human insulin, 0.01 M HCl, 0.007 M zinc acetate, 0.05 M sodium citrate, 17% acetone, 1.0 M NaCl. pH 6.3, SLOW COOLING at 298K
Crystal grow
*PLUS
Method: microgravity
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlinsulin11
20.01 M11HCl
30.007 Mzinc acetate11
40.05 Msodium citrate11
517 %acetone11
61.0 M11NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.8 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 1999
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.3→31.8 Å / Num. all: 41901 / Num. obs: 41901 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 48.8
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 8.6 / Num. unique all: 2792 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 912730 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1trz

1trz


Resolution: 1.3→31.8 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 4231 10 %Random
Rwork0.176 ---
all-41901 --
obs-41901 100 %-
Solvent computationSolvent model: flat model / Bsol: 55 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20.18 Å20 Å2
2---0.5 Å20 Å2
3---1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.3→31.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 24 212 1809
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.92
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.872
X-RAY DIFFRACTIONc_mcangle_it2.662.5
X-RAY DIFFRACTIONc_scbond_it2.162.5
X-RAY DIFFRACTIONc_scangle_it2.733
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 688 11.1 %
Rwork0.209 6219 -
obs-6219 100 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 31.8 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
X-RAY DIFFRACTIONc_mcbond_it1.872
X-RAY DIFFRACTIONc_scbond_it2.162.5
X-RAY DIFFRACTIONc_mcangle_it2.662.5
X-RAY DIFFRACTIONc_scangle_it2.733
LS refinement shell
*PLUS
Rfactor Rfree: 0.236 / % reflection Rfree: 11.1 % / Rfactor Rwork: 0.209

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