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- PDB-3inc: Crystal structure of human insulin with Ni+2 complex -

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Basic information

Entry
Database: PDB / ID: 3inc
TitleCrystal structure of human insulin with Ni+2 complex
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / Insulin / conformational state / metal binding / Carbohydrate metabolism / Cleavage on pair of basic residues / Diabetes mellitus / Disease mutation / Disulfide bond / Glucose metabolism / Secreted
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 fatty acid metabolic process / negative regulation of feeding behavior / 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 fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / 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 / regulation of amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of gluconeogenesis / negative regulation of lipid catabolic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / Insulin receptor recycling / transport vesicle / insulin-like growth factor receptor binding / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / Regulation of insulin secretion / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / cell-cell signaling / insulin receptor signaling pathway / glucose homeostasis / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / 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-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
NICKEL (II) ION / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRaghavendra, N. / Pattabhi, V. / Rajan, S.S.
CitationJournal: To be Published
Title: Metal induced conformational changes in human insulin: Crystal structures of Sr+2, Ni+2 and Cu+2 complexes of human insulin
Authors: Raghavendra, N. / Pattabhi, V. / Rajan, S.S.
History
DepositionAug 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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)11,7536
Polymers11,6354
Non-polymers1172
Water88349
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)35,25818
Polymers34,90612
Non-polymers3526
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 area19760 Å2
ΔGint-186 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.654, 81.654, 33.767
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-31-

NI

21D-31-

NI

31B-35-

HOH

41B-49-

HOH

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Components

#1: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 33.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2M Sodium Citrate, 0.12M Nickel Chloride, 1M Ammonium Sulphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 11, 2008 / Details: Mirrors
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→30.47 Å / Num. all: 7167 / Num. obs: 6787 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.07 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.094 / Net I/σ(I): 4.5
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.025 / Mean I/σ(I) obs: 1.1 / Num. unique all: 6787 / Rsym value: 0.1742 / % possible all: 97

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MSO

1mso


Resolution: 1.85→30.47 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.363 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25699 333 4.7 %RANDOM
Rwork0.20328 ---
obs0.20571 6787 99.36 %-
all-7167 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.246 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 2 49 861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022832
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.9541130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.42598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4924.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63515130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.163152
X-RAY DIFFRACTIONr_chiral_restr0.1470.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02636
X-RAY DIFFRACTIONr_nbd_refined0.2470.2393
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.210
X-RAY DIFFRACTIONr_mcbond_it1.5481.5516
X-RAY DIFFRACTIONr_mcangle_it2.0382810
X-RAY DIFFRACTIONr_scbond_it3.4613359
X-RAY DIFFRACTIONr_scangle_it4.2054.5320
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0.25699 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 24 -
Rwork0.261 492 -
obs-6787 100 %

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