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- PDB-5ems: Crystal Structure of an iodinated insulin analog -

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Basic information

Entry
Database: PDB / ID: 5ems
TitleCrystal Structure of an iodinated insulin analog
Components(Insulin) x 2
KeywordsHORMONE / insulin / non-standard modification / protein design / protein engineering
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 / Signaling by Insulin receptor / negative regulation of feeding behavior / 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 / Signaling by Insulin receptor / negative regulation of feeding behavior / 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 / positive regulation of protein autophosphorylation / 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 / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / Signal attenuation / fatty acid homeostasis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / COPI-mediated anterograde transport / transport vesicle / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / 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 nitric-oxide synthase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / positive regulation of glycolytic process / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / endosome lumen / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of cell differentiation / Regulation of insulin secretion / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / 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 / protease binding / positive regulation of cell growth / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLawrence, M.C. / Pandyarajan, V. / Wan, Z. / Weiss, M.A.
Funding support United States, Australia, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK04949 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK079233 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)F30 DK094685-04 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007250 United States
National Health and Medical Research Council (NHMRC, Australia)1005896 Australia
National Health and Medical Research Council (NHMRC, Australia)1058233 Australia
National Health and Medical Research Council (NHMRC, Australia)361646 Australia
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Extending Halogen-based Medicinal Chemistry to Proteins: IODO-INSULIN AS A CASE STUDY.
Authors: El Hage, K. / Pandyarajan, V. / Phillips, N.B. / Smith, B.J. / Menting, J.G. / Whittaker, J. / Lawrence, M.C. / Meuwly, M. / Weiss, M.A.
History
DepositionNov 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Jan 11, 2017Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.8Nov 20, 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
G: Insulin
H: Insulin
I: Insulin
J: Insulin
K: Insulin
L: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,33222
Polymers35,56512
Non-polymers76610
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18580 Å2
ΔGint-235 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.430, 61.630, 58.580
Angle α, β, γ (deg.)90.00, 111.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
Insulin


Mass: 2383.698 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide
Insulin


Mass: 3543.827 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 4 types, 85 molecules

#3: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate, 0.08% zinc acetate, 2% phenol

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Data collection

DiffractionMean temperature: 233 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40.85 Å / Num. obs: 13255 / % possible obs: 95.6 % / Redundancy: 4.76 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZNJ

1znj


Resolution: 2.3→40.847 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 1330 10.03 %
Rwork0.1626 --
obs0.1696 11926 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→40.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 46 75 2426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082411
X-RAY DIFFRACTIONf_angle_d1.0893234
X-RAY DIFFRACTIONf_dihedral_angle_d12.56796
X-RAY DIFFRACTIONf_chiral_restr0.051350
X-RAY DIFFRACTIONf_plane_restr0.006415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.32391070.2471978X-RAY DIFFRACTION78
2.3822-2.47750.30071290.2071151X-RAY DIFFRACTION92
2.4775-2.59030.25921300.18951165X-RAY DIFFRACTION95
2.5903-2.72680.33881350.18761200X-RAY DIFFRACTION96
2.7268-2.89760.31811340.1921204X-RAY DIFFRACTION99
2.8976-3.12130.28581390.19031239X-RAY DIFFRACTION100
3.1213-3.43520.24381350.16851242X-RAY DIFFRACTION100
3.4352-3.9320.19741360.14141239X-RAY DIFFRACTION100
3.932-4.95250.17071460.12911235X-RAY DIFFRACTION100
4.9525-40.85370.1931390.14461273X-RAY DIFFRACTION99
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)
18.0317-0.1511-0.68376.1314-2.00836.1787-0.1747-0.85470.38360.6966-0.1331-0.735-0.38710.76610.24820.36510.0297-0.13850.529-0.09280.4008-5.08383.414757.6567
23.282-4.9638-2.85918.2933.0855.4659-0.303-0.2581-0.05110.43050.1534-0.42230.62290.44550.18820.31940.0047-0.05740.2492-0.00640.4047-11.273-2.191153.1423
33.38680.1176-1.41199.1-3.52782.3892-0.1701-0.0893-0.6119-0.96030.10820.33370.3794-0.01010.1490.438-0.012-0.01530.23460.0260.3391-17.3679-18.390147.2766
46.474-1.9576-1.07493.82651.11763.2617-0.2487-0.3243-0.40040.5327-0.0488-0.13160.56980.43190.38680.37360.02610.02650.32460.03730.3132-13.4056-10.149248.8043
56.37750.3549-0.61495.2947-0.50922.97290.09020.23960.7545-0.0058-0.2766-0.1994-0.7664-0.14430.02770.3298-0.0239-0.0080.28770.13410.4458-14.32917.138133.8272
64.5425-0.1396-2.05873.67920.32372.7578-0.2164-0.0760.55050.1262-0.0738-0.0891-0.17890.23440.22360.26940.0321-0.01610.29690.04020.4353-10.10729.995137.4427
73.64563.01832.21414.85621.85455.02690.22580.5741-0.09980.29250.2474-0.70830.4520.532-0.51880.26860.0454-0.01620.4436-0.00380.61133.2811-2.279837.0966
83.59022.96811.74427.82225.65588.40220.12270.12990.3937-0.28790.0828-0.3862-0.37330.4428-0.22220.24420.03380.02980.28590.0380.4912-4.4482.454835.0215
95.7104-1.23133.98865.24772.59618.1488-0.0057-0.4505-0.13790.4419-0.09960.67060.2183-0.84780.03210.25350.03820.10470.36340.00920.3732-32.4233-0.777748.7411
107.45363.30693.67175.15262.74934.9282-0.1460.26850.1120.1999-0.16350.7107-0.1251-0.14450.33540.195-0.02260.02690.3249-0.03630.2894-27.046-0.04240.8898
112.5839-0.4117-1.77018.0427-0.68617.28170.34170.92510.2371-0.9083-0.32670.3319-0.1072-0.65760.00020.32260.0909-0.05990.4251-0.01770.3249-22.4608-2.014423.6534
124.1133-3.41950.34293.72860.31735.38380.17670.7699-0.0742-0.0495-0.28370.6088-0.0702-0.25280.10270.2649-0.0187-0.01570.353-0.00760.3473-23.5905-3.15332.7744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'
7X-RAY DIFFRACTION7chain 'G'
8X-RAY DIFFRACTION8chain 'H'
9X-RAY DIFFRACTION9chain 'I'
10X-RAY DIFFRACTION10chain 'J'
11X-RAY DIFFRACTION11chain 'K'
12X-RAY DIFFRACTION12chain 'L'

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