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- PDB-6gnq: Monoclinic crystalline form of human insulin, complexed with meta... -

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Basic information

Entry
Database: PDB / ID: 6gnq
TitleMonoclinic crystalline form of human insulin, complexed with meta-cresol
Components(Insulin) x 2
KeywordsHORMONE / human insulin / meta-cresol / hexamer / 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 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
M-CRESOL / isothiocyanate / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMargiolaki, I. / Karavassili, F. / Valmas, A. / Dimarogona, M. / Giannopoulou, A.E. / Fili, S. / Schluckebier, G. / Norrman, M. / Beckers, D. / Fitch, A.N.
Funding support Greece, 2items
OrganizationGrant numberCountry
European UnionBioStruct-X,No.283570 Greece
"General Secretariat for Research and Technology (GSRT) - Hellenic Foundation for Research and Innovation2467 Greece
CitationJournal: To Be Published
Title: Monoclinic crystalline form of human insulin, complexed with meta-cresol
Authors: Margiolaki, I. / Karavassili, F. / Valmas, A. / Dimarogona, M. / Giannopoulou, A.E. / Fili, S. / Schluckebier, G. / Norrman, M. / Beckers, D. / Fitch, A.N.
History
DepositionMay 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
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_asym_id / _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.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_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.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_conn.ptnr2_label_seq_id

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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
E: Insulin
F: Insulin
G: Insulin
H: Insulin
I: Insulin
J: Insulin
K: Insulin
L: Insulin
M: Insulin
N: Insulin
O: Insulin
P: Insulin
Q: Insulin
R: Insulin
S: Insulin
T: Insulin
U: Insulin
V: Insulin
W: Insulin
X: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,22854
Polymers69,81224
Non-polymers2,41630
Water1,74797
1
A: Insulin
B: Insulin
C: Insulin
D: Insulin
E: Insulin
F: Insulin
G: Insulin
H: Insulin
I: Insulin
J: Insulin
K: Insulin
L: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,17628
Polymers34,90612
Non-polymers1,27016
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20860 Å2
ΔGint-182 kcal/mol
Surface area12780 Å2
MethodPISA
2
M: Insulin
N: Insulin
O: Insulin
P: Insulin
Q: Insulin
R: Insulin
S: Insulin
T: Insulin
U: Insulin
V: Insulin
W: Insulin
X: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,05226
Polymers34,90612
Non-polymers1,14614
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19760 Å2
ΔGint-188 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.662, 70.361, 84.748
Angle α, β, γ (deg.)90.00, 105.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX

#1: Protein/peptide
Insulin


Mass: 2383.698 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#2: Protein/peptide
Insulin


Mass: 3433.953 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: The missing amino acids were not included in the pdb file because there was no electron density in the corresponding position.
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308

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Non-polymers , 5 types, 127 molecules

#3: Chemical
ChemComp-CRS / M-CRESOL


Mass: 108.138 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C7H8O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-IS8 / isothiocyanate


Mass: 59.090 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHNS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 6.1
Details: sodium-monopotassium phosphate buffer, zinc acetate, m-cresol
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 2.2→81.78 Å / Num. obs: 27332 / % possible obs: 99.1 % / Redundancy: 6.4 % / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.052 / Rrim(I) all: 0.134

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1znj

1znj


Resolution: 2.2→81.78 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.89 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.438 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 1310 4.8 %RANDOM
Rwork0.22301 ---
obs0.22569 26006 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.747 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.11 Å2
2---1.12 Å20 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 2.2→81.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4634 0 152 97 4883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194910
X-RAY DIFFRACTIONr_bond_other_d0.0010.024227
X-RAY DIFFRACTIONr_angle_refined_deg0.9021.9726620
X-RAY DIFFRACTIONr_angle_other_deg0.70339820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3695566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75224.678233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92715758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.011512
X-RAY DIFFRACTIONr_chiral_restr0.0570.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021030
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7364.1582332
X-RAY DIFFRACTIONr_mcbond_other1.7344.1572327
X-RAY DIFFRACTIONr_mcangle_it3.0096.1972869
X-RAY DIFFRACTIONr_mcangle_other3.0086.1982870
X-RAY DIFFRACTIONr_scbond_it1.6174.412578
X-RAY DIFFRACTIONr_scbond_other1.6144.412574
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8056.5413747
X-RAY DIFFRACTIONr_long_range_B_refined5.27749.1735731
X-RAY DIFFRACTIONr_long_range_B_other5.27649.185732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 81 -
Rwork0.286 1791 -
obs--91.81 %

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