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- PDB-2w44: Structure DeltaA1-A4 insulin -

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Basic information

Entry
Database: PDB / ID: 2w44
TitleStructure DeltaA1-A4 insulin
Components(INSULIN) x 2
KeywordsHORMONE / INSULIN
Function / homology
Function and homology information


cellular response to oxygen-containing compound / 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 / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion ...cellular response to oxygen-containing compound / 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 / regulation of protein secretion / Insulin processing / 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 / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / 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 / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / 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 cytokine production / positive regulation of glycolytic process / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / Regulation of insulin secretion / positive regulation of cell differentiation / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / Golgi lumen / positive regulation of protein localization to nucleus / vasodilation / cognition / glucose metabolic process / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / 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
RESORCINOL / Insulin / Insulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsThorsoee, K.S. / Schlein, M. / Brandt, J. / Schluckebier, G. / Naver, H.
CitationJournal: Biochemistry / Year: 2010
Title: Kinetic Evidence for the Sequential Association of Insulin Binding Sites 1 and 2 to the Insulin Receptor and the Influence of Receptor Isoform.
Authors: Thorsoe, K.S. / Schlein, M. / Steensgaard, D.B. / Brandt, J. / Schluckebier, G. / Naver, H.
History
DepositionNov 21, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 22, 2013Group: Database references / Derived calculations
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,38511
Polymers15,9546
Non-polymers4315
Water79344
1
A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
E: INSULIN
F: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
E: INSULIN
F: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,77122
Polymers31,90912
Non-polymers86210
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area17900 Å2
ΔGint-219.5 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.050, 88.620, 73.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein/peptide , 2 types, 6 molecules ACEBDF

#1: Protein/peptide INSULIN / INS


Mass: 1985.244 Da / Num. of mol.: 3 / Fragment: RESIDUES 82-98
Source method: isolated from a genetically manipulated source
Details: HUMAN INSULIN WITH A-CHAIN RESIDUES 1-4 DELETION / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: A6XGL2, UniProt: P01308*PLUS
#2: Protein/peptide INSULIN


Mass: 3332.849 Da / Num. of mol.: 3 / Fragment: RESIDUES 25-53
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: A6XGL2, UniProt: P01308*PLUS

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Non-polymers , 4 types, 49 molecules

#3: Chemical ChemComp-RCO / RESORCINOL / 1,3-BENZENEDIOL / 1,3-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7
Details: 150 MM NA/K-PHOSPHATE PH 7.0 AND 7.5 % (V/V) ETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→28 Å / Num. obs: 8261 / % possible obs: 87.6 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7 / % possible all: 53.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0053refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7INS

7ins


Resolution: 2→28.34 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.965 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.258 461 5.6 %RANDOM
Rwork0.205 ---
obs0.208 7800 87.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2--0.76 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 26 44 1152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211172
X-RAY DIFFRACTIONr_bond_other_d0.0010.02769
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9711596
X-RAY DIFFRACTIONr_angle_other_deg1.0233.021843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3345140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29724.13858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5315179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.077154
X-RAY DIFFRACTIONr_chiral_restr0.1090.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021309
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02259
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_it0.7941.5687
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44221104
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2893485
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5624.5487
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.264 20
Rwork0.225 358
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.9995-3.67960.68239.8393-3.36489.9383-0.30790.1892-0.36540.18770.45530.50891.2152-1.8239-0.14730.1933-0.23820.02560.34540.01980.14837.1454.24820.717
24.76580.70662.42095.063-2.516916.14820.05440.0153-0.3518-0.1361-0.1069-0.20881.0518-0.23950.05250.0721-0.02010.01450.0138-0.01250.064815.1246.0617.982
32.8427-0.7169-2.31744.505-2.59817.3330.06680.1009-0.0412-0.3722-0.2270.5621-0.2149-1.22410.16030.30690.1947-0.03650.2115-0.03970.33359.94933.32918.197
46.25785.79922.735211.46867.1047.26820.2075-0.13760.33840.3599-0.20460.2981-0.366-0.6188-0.00290.14020.10230.0360.10130.03010.073212.06425.38622.337
515.24445.75722.2446.32093.10575.4849-0.03911.4874-0.402-0.82520.18180.2198-0.4508-0.1443-0.14270.28470.0324-0.0390.26940.00220.157326.50615.4260.827
611.28650.20180.12898.03140.42987.04820.220.54240.5037-0.2912-0.310.0635-0.23920.23390.090.02270.01390.00340.04840.02870.037127.36820.998.287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 21
2X-RAY DIFFRACTION2B1 - 29
3X-RAY DIFFRACTION3C5 - 21
4X-RAY DIFFRACTION4D1 - 28
5X-RAY DIFFRACTION5E5 - 21
6X-RAY DIFFRACTION6F2 - 29

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