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- PDB-1fub: FIRST PROTEIN STRUCTURE DETERMINED FROM X-RAY POWDER DIFFRACTION DATA -

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Basic information

Entry
Database: PDB / ID: 1fub
TitleFIRST PROTEIN STRUCTURE DETERMINED FROM X-RAY POWDER DIFFRACTION DATA
Components
  • INSULIN, A CHAIN
  • INSULIN, B CHAIN
KeywordsHORMONE/GROWTH FACTOR / POWDER DIFFRACTION / RIETVELD REFINEMENT / INSULIN / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / 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 ...negative regulation of NAD(P)H oxidase activity / 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 protein autophosphorylation / Regulation of gene expression in beta cells / positive regulation of respiratory burst / negative regulation of acute inflammatory response / regulation of transmembrane transporter activity / 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 / positive regulation of insulin receptor signaling pathway / negative regulation of gluconeogenesis / 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 / 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 / positive regulation of long-term synaptic potentiation / endosome lumen / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / negative regulation of protein catabolic process / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / Golgi lumen / positive regulation of protein localization to nucleus / cognition / glucose metabolic process / vasodilation / 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
Similarity search - Domain/homology
MethodPOWDER DIFFRACTION / SYNCHROTRON
AuthorsVon Dreele, R.B. / Stephens, P.W. / Blessing, R.H. / Smith, G.D.
Citation
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.
#1: Journal: J.Appl.Crystallogr. / Year: 1999
Title: Combined Rietveld and Stereochemical Restraint Refinement of a Protein Crystal Structure
Authors: Von Dreele, R.B.
#2: Journal: Biochemistry / Year: 1994
Title: Crystallographic Evidence for Dual Coordinate Aroun in the T3R3 Human Insulin Hexamer
Authors: Smith, G.D. / Ciszak, E.
History
DepositionSep 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Oct 3, 2018Group: Atomic model / Data collection / Category: atom_site / Item: _atom_site.occupancy
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_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

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Assembly

Deposited unit
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)11,8609
Polymers11,6354
Non-polymers2255
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)35,58027
Polymers34,90612
Non-polymers67415
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area19170 Å2
ΔGint-351 kcal/mol
Surface area13000 Å2
MethodPISA, PQS
Components on special symmetry positions
IDModelComponents
11B-501-

ZN

21B-502-

CL

31B-503-

NA

41D-1501-

ZN

51D-1502-

CL

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Components

#1: Protein/peptide INSULIN, A CHAIN


Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: A CHAIN OF T3R3 VARIANT / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: P01308
#2: Protein/peptide INSULIN, B CHAIN


Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: B CHAIN OF T3R3 VARIANT / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: P01308
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: POWDER DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 300 K / Method: grinding / Details: grinding, temperature 300K
Crystal grow
*PLUS
Method: unknown / Details: ground into powder
Components of the solutions
*PLUS
Conc.: 1.0 M / Chemical formula: NaCl

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3B1 / Wavelength: 0.700233
DetectorType: OTHER / Detector: DIFFRACTOMETER / Date: Oct 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.700233 Å / Relative weight: 1

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