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- PDB-2vjz: Crystal structure form ultalente insulin microcrystals -

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Basic information

Entry
Database: PDB / ID: 2vjz
TitleCrystal structure form ultalente insulin microcrystals
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / MICRO FOCUS BEAMLINE / INSULIN / SECRETED / MICRO CRYSTAL / CLEAVAGE ON PAIR OF BASIC RESIDUES / DISEASE MUTATION / DIABETES MELLITUS
Function / homology
Function and homology information


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 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 / activation of protein kinase B activity / negative regulation of respiratory burst involved in inflammatory response / 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 / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / 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 glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import across plasma membrane / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / cognition / vasodilation / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWagner, A. / Diez, J. / Schulze-Briese, C. / Schluckebier, G.
CitationJournal: Proteins / Year: 2009
Title: Crystal Structure of Ultralente-A Microcrystalline Insulin Suspension.
Authors: Wagner, A. / Diez, J. / Schulze-Briese, C. / Schluckebier, G.
History
DepositionDec 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 18, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_database_status.status_code_sf / _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_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_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.ptnr1_symmetry / _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
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 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 A CHAIN
B: INSULIN B CHAIN
C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,90810
Polymers11,6354
Non-polymers2736
Water1,74797
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)35,72430
Polymers34,90612
Non-polymers81818
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 area20080 Å2
ΔGint-138 kcal/mol
Surface area17040 Å2
MethodPQS
Unit cell
Length a, b, c (Å)79.820, 79.820, 36.710
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-1030-

ZN

21B-1031-

CL

31D-2005-

HOH

41D-2009-

HOH

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Components

#1: Protein/peptide INSULIN A CHAIN


Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: RESIDUES 90-110
Source method: isolated from a genetically manipulated source
Details: PRECURSOR CRYSTALS ULTRALENTE INSULIN CRYSTALS PROCESS
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308
#2: Protein/peptide INSULIN B CHAIN


Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-54
Source method: isolated from a genetically manipulated source
Details: PRECURSOR CRYSTALS FROM THE ULTRALENTE PROCESS / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9183
DetectorType: MARRESEARCH / Detector: CCD / Details: MICRO FOCUS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 1.8→32.4 Å / Num. obs: 33133 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.8 / % possible all: 84.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TRZ

1trz


Resolution: 1.8→32.43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.558 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STURCTURE DETERMINATION FROM MICROCRYSTALS 8 X8 X 3 MICRO METER
RfactorNum. reflection% reflectionSelection details
Rfree0.239 391 5 %RANDOM
Rwork0.172 ---
obs0.175 7433 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms785 0 6 97 888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022828
X-RAY DIFFRACTIONr_bond_other_d0.0010.02536
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9491129
X-RAY DIFFRACTIONr_angle_other_deg0.9593.0191296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63524.63441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80715129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.904152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02175
X-RAY DIFFRACTIONr_nbd_refined0.2050.2219
X-RAY DIFFRACTIONr_nbd_other0.1810.2531
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2414
X-RAY DIFFRACTIONr_nbtor_other0.090.2383
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2760.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4140.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9361.5653
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0852804
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0613419
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5454.5323
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 22
Rwork0.335 419
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)
15.5418-2.08712.26626.53160.93643.2099-0.1243-0.48830.0490.3847-0.03510.3995-0.0139-0.58440.1594-0.27470.02580.0497-0.115-0.0089-0.2499-17.56663.236733.5188
24.6598-1.04211.70195.3527-0.96777.9794-0.0019-0.1362-0.11690.1756-0.0738-0.0205-0.0298-0.22190.0757-0.3311-0.00630.0193-0.28350.0079-0.294-12.50883.425927.9657
38.81590.6436-2.490212.26480.10862.6706-0.00160.59730.1725-1.0047-0.06080.2946-0.4975-0.38620.0624-0.10910.05490.0029-0.23240.0538-0.2548-3.010516.295615.9487
43.79561.45320.88666.71194.79337.81830.10180.13330.0218-0.264-0.04620.0888-0.2963-0.4556-0.0555-0.29020.00150.0321-0.27570.0505-0.2632-6.68039.303719.9222
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2B1 - 29
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION4D1 - 28

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