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- PDB-5uss: Insulin with proline analog PiP at position B28 in the R6 state -

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Basic information

Entry
Database: PDB / ID: 5uss
TitleInsulin with proline analog PiP at position B28 in the R6 state
Components(Insulin Chain ...) x 2
KeywordsHORMONE / 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 / 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 ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic 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 respiratory burst / positive regulation of peptide hormone secretion / 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 / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / 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 / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / wound healing / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.061 Å
AuthorsLieblich, S.A. / Fang, K.Y. / Tirrell, D.A.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: To Be Published
Title: Insulin with proline analog PiP at position B28 in the R6 state
Authors: Lieblich, S.A. / Fang, K.Y. / Tirrell, D.A.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
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.ptnr2_symmetry / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin Chain A
B: Insulin Chain B
C: Insulin Chain A
D: Insulin Chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,05310
Polymers11,6634
Non-polymers3906
Water181
1
A: Insulin Chain A
B: Insulin Chain B
C: Insulin Chain A
D: Insulin Chain B
hetero molecules

A: Insulin Chain A
B: Insulin Chain B
C: Insulin Chain A
D: Insulin Chain B
hetero molecules

A: Insulin Chain A
B: Insulin Chain B
C: Insulin Chain A
D: Insulin Chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,16030
Polymers34,99012
Non-polymers1,17018
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17690 Å2
ΔGint-327 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.024, 79.024, 39.509
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
11B-101-

ZN

21B-102-

CL

31D-101-

ZN

41D-102-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASNASNchain AAA1 - 211 - 21
21GLYGLYASNASNchain CCC1 - 211 - 21
12VALVALYCPYCPchain BBB2 - 282 - 28
22PHEPHEYCPYCPchain DDD1 - 281 - 28

NCS ensembles :
ID
1
2

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Components

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Insulin Chain ... , 2 types, 4 molecules ACBD

#1: Protein/peptide Insulin Chain A


Mass: 2383.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide Insulin Chain B


Mass: 3447.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308

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Non-polymers , 4 types, 7 molecules

#3: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 2 / 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.: 1 / 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: 2.04 Å3/Da / Density % sol: 39.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 300mM Tris pH 8, 17mM Zinc Acetate, 1% phenol, 313mM Sodium Citrate, 11.25% Acetone
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2016
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→25.87 Å / Num. obs: 9265 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 42.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.026 / Rrim(I) all: 0.061 / Net I/σ(I): 12.9 / Num. measured all: 49116 / Scaling rejects: 97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.75-1.785.13.26725204930.2841.6043.6460.499.8
9.1-25.8760.038398660.9980.0170.04252.296.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.86 Å25.87 Å
Translation4.86 Å25.87 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.27data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.22data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EV6

1ev6


Resolution: 2.061→25.866 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 256 4.51 %
Rwork0.1686 5417 -
obs0.1709 5673 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.79 Å2 / Biso mean: 48.8064 Å2 / Biso min: 27.35 Å2
Refinement stepCycle: final / Resolution: 2.061→25.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms700 0 18 1 719
Biso mean--38.25 49.05 -
Num. residues----97
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009733
X-RAY DIFFRACTIONf_angle_d1.08983
X-RAY DIFFRACTIONf_chiral_restr0.051113
X-RAY DIFFRACTIONf_plane_restr0.005125
X-RAY DIFFRACTIONf_dihedral_angle_d12.669232
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A162X-RAY DIFFRACTION0.938TORSIONAL
12C162X-RAY DIFFRACTION0.938TORSIONAL
21B200X-RAY DIFFRACTION0.938TORSIONAL
22D200X-RAY DIFFRACTION0.938TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0614-2.59680.29281370.23427022839
2.5968-25.86780.20381190.153327152834
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)
11.92860.09860.2117.89390.63716.78660.03050.71260.3857-0.89860.38170.2631-0.61720.0868-0.62530.6509-0.01140.14950.51690.0870.51064.073213.1763-12.3477
22.4958-1.44750.15662.16421.058.7788-0.02280.14171.2891-0.3414-0.1268-0.0325-1.22460.28870.20760.6445-0.07550.02820.37760.04640.69646.777418.5013-3.5091
35.09631.61971.28339.15571.88185.3913-0.18310.27690.7326-0.1692-0.11430.4163-0.2895-0.14580.40450.35420.01970.02760.32630.02790.31561.06029.7704-2.6419
42.01131.55385.27538.72744.25314.14230.1790.26142.75190.0078-0.7272-0.1920.17620.2912-0.11330.67350.05950.14690.39210.07580.5182-2.376117.2366-2.1219
50.40271.31560.39579.3428-1.65382.1472-0.5293-0.37370.23521.64740.3961.2149-1.03960.2238-0.15730.82870.15890.11930.7691-0.00150.3946-8.52312.648913.5275
63.37021.36142.23294.1184-0.6754.23490.4413-1.22530.71911.0591-0.01810.0434-0.5838-0.799-0.27790.62050.14170.19710.73020.07690.477-11.00216.931613.9234
76.72262.5040.26657.9437-0.86745.5907-0.0474-0.05040.79660.0513-0.01240.5329-0.7046-1.20840.12780.56590.2190.09320.6121-0.03550.7025-15.157512.66234.7863
84.331-1.4421.5797.6249-2.33915.382-0.37270.04750.77090.3717-0.0453-0.0919-0.73530.12270.49230.34880.00710.04090.3213-0.01750.3511-5.05468.31554.4602
95.3742-3.68335.15092.5344-3.51235.1317-0.1120.00052.0340.6848-0.0761-0.7356-1.0314-0.7690.19880.65730.12060.07860.39940.05490.6649-5.158817.05152.9066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )A1 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 21 )A13 - 21
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 22 )B2 - 22
4X-RAY DIFFRACTION4chain 'B' and (resid 23 through 27 )B23 - 27
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 6 )C1 - 6
6X-RAY DIFFRACTION6chain 'C' and (resid 7 through 12 )C7 - 12
7X-RAY DIFFRACTION7chain 'C' and (resid 13 through 21 )C13 - 21
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 22 )D1 - 22
9X-RAY DIFFRACTION9chain 'D' and (resid 23 through 27 )D23 - 27

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