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- PDB-1trz: CRYSTALLOGRAPHIC EVIDENCE FOR DUAL COORDINATION AROUND ZINC IN TH... -

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Entry
Database: PDB / ID: 1trz
TitleCRYSTALLOGRAPHIC EVIDENCE FOR DUAL COORDINATION AROUND ZINC IN THE T3R3 HUMAN INSULIN HEXAMER
Components(INSULIN) x 2
KeywordsHORMONE
Function / homology
Function and homology information


negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process / 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 glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process / 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 / 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 / activation of protein kinase B activity / 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 / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / transport vesicle / nitric oxide-cGMP-mediated signaling / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / endosome lumen / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / 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 / 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 / Resolution: 1.6 Å
AuthorsCiszak, E. / Smith, G.D.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystallographic evidence for dual coordination around zinc in the T3R3 human insulin hexamer.
Authors: Ciszak, E. / Smith, G.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984
Title: Structural Stability in the 4-Zinc Human Insulin Hexamer
Authors: Smith, G.D. / Swenson, D.C. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D.
#2: Journal: Nature / Year: 1976
Title: Structure of Insulin in 4-Zinc Insulin
Authors: Bentley, G. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D. / Mercola, D.
History
DepositionNov 19, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn / diffrn_detector / diffrn_radiation_wavelength / diffrn_source / entity / exptl / exptl_crystal / exptl_crystal_grow / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_conn_angle / refine / refine_hist / reflns / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.src_method / _exptl.crystals_number / _exptl_crystal.description / _pdbx_database_status.process_site / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine.ls_d_res_low / _refine.ls_number_reflns_obs / _refine_hist.d_res_low / _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.ptnr1_symmetry / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8609
Polymers11,6354
Non-polymers2255
Water2,216123
1
A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9194
Polymers5,8182
Non-polymers1012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-13 kcal/mol
Surface area3420 Å2
MethodPISA
2
C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9425
Polymers5,8182
Non-polymers1243
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-12 kcal/mol
Surface area3930 Å2
MethodPISA
3
A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)35,58027
Polymers34,90612
Non-polymers67415
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 area18090 Å2
ΔGint-319 kcal/mol
Surface area12680 Å2
MethodPISA
4
A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,58027
Polymers34,90612
Non-polymers67415
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_554-y,x-y,z-11
crystal symmetry operation3_554-x+y,-x,z-11
Buried area12640 Å2
ΔGint-280 kcal/mol
Surface area18120 Å2
MethodPISA
5
C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,58027
Polymers34,90612
Non-polymers67415
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_556-y,x-y,z+11
crystal symmetry operation3_556-x+y,-x,z+11
Buried area13550 Å2
ΔGint-337 kcal/mol
Surface area17590 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-35 kcal/mol
Surface area5950 Å2
MethodPISA
7
A: INSULIN
B: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8609
Polymers11,6354
Non-polymers2255
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3650 Å2
ΔGint-34 kcal/mol
Surface area6460 Å2
MethodPISA
8
C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,82515
Polymers17,4536
Non-polymers3729
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5600 Å2
ΔGint-147 kcal/mol
Surface area9930 Å2
MethodPISA
9
A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,75612
Polymers17,4536
Non-polymers3036
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5590 Å2
ΔGint-118 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.638, 80.638, 37.782
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-31-

ZN

21B-32-

CL

31D-31-

ZN

41D-32-

CL

51B-34-

HOH

61B-36-

HOH

71D-34-

HOH

81D-35-

HOH

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide INSULIN


Mass: 2383.698 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Crystalline biosynthetic human insulin / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide INSULIN


Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Crystalline biosynthetic human insulin / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 4 types, 128 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE CONFORMATIONS OF TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A CHANGE IN CONFORMATION OF THE ...THE CONFORMATIONS OF TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A CHANGE IN CONFORMATION OF THE FIRST EIGHT RESIDUES OF THE B-CHAINS. IN MONOMER I, B 1 - B 8 ADOPT AN EXTENDED CONFORMATION WHILE IN MONOMER II THIS SEGMENT ADOPTS AN ALPHA-HELICAL CONFORMATION, DISRUPTED AT B 3 AND B 2.
Has protein modificationY
Nonpolymer detailsEACH OF TWO ZINC IONS IS COORDINATED BY THE THREE SYMMETRY RELATED B 10 HIS. THE COORDINATION ...EACH OF TWO ZINC IONS IS COORDINATED BY THE THREE SYMMETRY RELATED B 10 HIS. THE COORDINATION SPHERE OF THE ZN1 IS EITHER TETRAHEDRAL WITH THE FOURTH SITE FILLED BY A CL1 OR OCTAHEDRAL, COMPLETED BY THREE SYMMETRY RELATED HOH 1. THE COORDINATION OF ZN2 IS TETRAHEDRAL WITH EITHER CL2 OR A HOH 2.

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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: 2.03 Å3/Da / Density % sol: 39.45 % / Description: Colorless, sharp-edged rhombohedrons up to 1mm
Crystal growpH: 6.4
Details: Crystals were grown from 0.05M sodium citrate and 0.007M zinc acetate in the presence of 0.75M sodium chloride at pH6.4
Crystal grow
*PLUS
pH: 6.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.05 Msodium citrate11
20.007 Mzinc acetate11
30.75 M12NaCl

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Data collection

DiffractionMean temperature: 290 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS II / Wavelength: 1.541 / Wavelength: 1.541 Å
DetectorDetector: IMAGE PLATE
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionRmerge(I) obs: 0.054
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 11601 / Num. measured all: 34613 / Rmerge(I) obs: 0.054

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.6→8 Å
Details: SIDE CHAINS OF VAL D 2 (MON II), LYS B 29 AND THR B 30 OF BOTH MONOMERS ARE NOT INCLUDED IN THE MODEL. THE SIDE CHAINS OF B 109 AND B 105 ARE REFINED IN TWO ALTERNATE ORIENTATIONS.
RfactorNum. reflection
obs0.172 9225
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms798 0 5 123 926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d3
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 9225 / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.040.049
X-RAY DIFFRACTIONp_planar_d0.050.057
X-RAY DIFFRACTIONp_plane_restr0.020.014
X-RAY DIFFRACTIONp_chiral_restr0.150.159

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