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- PDB-3tt8: Crystal Structure Analysis of Cu Human Insulin Derivative -

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Basic information

Entry
Database: PDB / ID: 3tt8
TitleCrystal Structure Analysis of Cu Human Insulin Derivative
Components
  • INSULIN A-CHAIN
  • INSULIN B-CHAIN
KeywordsHORMONE / Cu insulin
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 / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / nitric oxide-cGMP-mediated signaling / IRS activation / Insulin processing / 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 / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / nitric oxide-cGMP-mediated signaling / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / positive regulation of nitric oxide mediated signal transduction / fatty acid homeostasis / regulation of protein localization to plasma membrane / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic 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 / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / activation of protein kinase B activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / Regulation of insulin secretion / acute-phase response / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of nitric-oxide synthase activity / positive regulation of cell differentiation / negative regulation of proteolysis / regulation of transmembrane transporter activity / wound healing / regulation of synaptic plasticity / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / Golgi lumen / positive regulation of protein localization to nucleus / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / 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
COPPER (II) ION / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.12 Å
AuthorsPrugovecki, B. / Matkovic-Calogovic, D.
CitationJournal: To be Published
Title: Crystal Structure Analysis of Cu Human Insulin Derivative
Authors: Prugovecki, B. / Matkovic-Calogovic, D.
History
DepositionSep 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7626
Polymers11,6354
Non-polymers1272
Water2,810156
1
A: INSULIN A-CHAIN
B: INSULIN B-CHAIN


Theoretical massNumber of molelcules
Total (without water)5,8182
Polymers5,8182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-16 kcal/mol
Surface area3700 Å2
MethodPISA
2
C: INSULIN A-CHAIN
D: INSULIN B-CHAIN


Theoretical massNumber of molelcules
Total (without water)5,8182
Polymers5,8182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-14 kcal/mol
Surface area3810 Å2
MethodPISA
3
A: INSULIN A-CHAIN
B: INSULIN B-CHAIN
C: INSULIN A-CHAIN
D: INSULIN B-CHAIN

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

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


Theoretical massNumber of molelcules
Total (without water)34,90612
Polymers34,90612
Non-polymers00
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 area18520 Å2
ΔGint-153 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.560, 81.560, 33.747
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
11E-1-

CU

21F-1-

CU

31B-164-

HOH

41D-93-

HOH

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Components

#1: Protein/peptide INSULIN A-CHAIN / Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide INSULIN B-CHAIN / Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.86 Å3/Da / Density % sol: 33.75 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.4
Details: 1mM sodium citrate, volume fractions of acetone 10% and 7.5 mM cooper(II) acetate monohydrate, pH 6.4, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→40.78 Å / Num. obs: 31826 / % possible obs: 97.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 15.1
Reflection shell
Redundancy (%)Num. measured allNum. unique allRsym valueDiffraction-ID
3.41492244110.3231
3.51599345160.2231
3.61508742070.1731
3.61414439100.1151
3.71333736320.0791
3.71219632790.061
3.71079028810.0421
3.7909824300.0331
3.6660718350.0291
321857250.0331

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.401 / Cor.coef. Fo:Fc: 0.505 / Cor.coef. Io to Ic: 0.46
Highest resolutionLowest resolution
Rotation3 Å16.927 Å
Translation3 Å16.927 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.1.20data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mso

1mso


Resolution: 1.12→24.14 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.981 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17902 1616 5.1 %RANDOM
Rwork0.13245 ---
obs0.13478 30207 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.364 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.12→24.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 2 156 968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.022904
X-RAY DIFFRACTIONr_bond_other_d0.0010.02569
X-RAY DIFFRACTIONr_angle_refined_deg2.071.9531244
X-RAY DIFFRACTIONr_angle_other_deg1.36731405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0642544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02115144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.499152
X-RAY DIFFRACTIONr_chiral_restr0.1290.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021038
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02190
X-RAY DIFFRACTIONr_mcbond_it2.6731.5549
X-RAY DIFFRACTIONr_mcbond_other3.4771.5221
X-RAY DIFFRACTIONr_mcangle_it3.7692896
X-RAY DIFFRACTIONr_scbond_it5.1663355
X-RAY DIFFRACTIONr_scangle_it7.164.5343
X-RAY DIFFRACTIONr_rigid_bond_restr2.9093904
LS refinement shellResolution: 1.12→1.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 116 -
Rwork0.335 2164 -
obs--95.4 %

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