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- PDB-1lph: LYS(B28)PRO(B29)-HUMAN INSULIN -

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Basic information

Entry
Database: PDB / ID: 1lph
TitleLYS(B28)PRO(B29)-HUMAN INSULIN
Components(INSULIN) x 2
KeywordsHORMONE / INSULIN ANALOGUE / GLUCOSE METABOLISM
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 / 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 / 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 / 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 / vasodilation / cognition / 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 / Resolution: 2.3 Å
AuthorsCiszak, E. / Beals, J.M. / Frank, B.H. / Baker, J.C. / Carter, N.D. / Smith, G.D.
Citation
Journal: Structure / Year: 1995
Title: Role of C-terminal B-chain residues in insulin assembly: the structure of hexameric LysB28ProB29-human insulin.
Authors: Ciszak, E. / Beals, J.M. / Frank, B.H. / Baker, J.C. / Carter, N.D. / Smith, G.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: The Structure of a Complex of Hexameric Insulin and 4'-Hydroxyacetanilide
Authors: Smith, G.D. / Ciszak, E.
#2: Journal: Biochemistry / Year: 1994
Title: Crystallographic Evidence for Dual Coordination Around Zinc in the T3R3 Human Insulin Hexamer
Authors: Ciszak, E. / Smith, G.D.
#3: 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.
History
DepositionApr 19, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)11,8968
Polymers11,6354
Non-polymers2604
Water1,06359
1
A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8833
Polymers5,8182
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-13 kcal/mol
Surface area3710 Å2
MethodPISA
2
C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0135
Polymers5,8182
Non-polymers1953
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-12 kcal/mol
Surface area4060 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)35,68724
Polymers34,90612
Non-polymers78112
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 area18830 Å2
ΔGint-269 kcal/mol
Surface area12910 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)35,68724
Polymers34,90612
Non-polymers78112
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 area12550 Å2
ΔGint-250 kcal/mol
Surface area19190 Å2
MethodPISA
5
D: INSULIN
hetero molecules

D: INSULIN
hetero molecules

D: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
C: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
C: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
C: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,68724
Polymers34,90612
Non-polymers78112
Water21612
TypeNameSymmetry operationNumber
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
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9310 Å2
ΔGint-214 kcal/mol
Surface area22430 Å2
MethodPISA
6
C: INSULIN
D: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8968
Polymers11,6354
Non-polymers2604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area3870 Å2
ΔGint-30 kcal/mol
Surface area6600 Å2
MethodPISA
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-32 kcal/mol
Surface area6320 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)18,03815
Polymers17,4536
Non-polymers5859
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 area5530 Å2
ΔGint-147 kcal/mol
Surface area10180 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)17,6499
Polymers17,4536
Non-polymers1963
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 area5480 Å2
ΔGint-90 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.620, 79.620, 37.780
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

21D-31-

ZN

31D-32-

CL

41B-39-

HOH

51D-42-

HOH

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide INSULIN / LYS(B28)PRO(B29)-HUMAN INSULIN


Mass: 2383.698 Da / Num. of mol.: 2 / Mutation: CHAIN B, D, P28K, K29P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide INSULIN / LYS(B28)PRO(B29)-HUMAN INSULIN


Mass: 3433.953 Da / Num. of mol.: 2 / Mutation: CHAIN B, D, P28K, K29P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 4 types, 63 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#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.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsEACH OF TWO ZINC IONS IS COORDINATED BY THE THREE SYMMETRY RELATED HIS B 10 SIDE CHAINS. THE ...EACH OF TWO ZINC IONS IS COORDINATED BY THE THREE SYMMETRY RELATED HIS B 10 SIDE CHAINS. THE COORDINATION SPHERE OF ZN B 31 IS OCTAHEDRAL WITH THE REMAINING THREE SITES FILLED BY WATER, HOH 1. THE COORDINATION OF ZN D 31 IS TETRAHEDRAL COMPLETED BY CL D 32.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 33 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.9 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.27 mMhuman insulin11
20.12 Mhydrochloric acid11
30.05 Msodium citrate11

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Data collection

DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 9, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→38.5 Å / Num. obs: 3910 / % possible obs: 83.4 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Num. measured all: 19299 / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
RIGAKUdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
PROLSQrefinement
RIGAKUdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.161 --
obs0.161 3548 75.7 %
Displacement parametersBiso mean: 37.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms795 0 10 59 864
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.1562.5
X-RAY DIFFRACTIONx_mcangle_it3.3872.5
X-RAY DIFFRACTIONx_scbond_it1.5551.5
X-RAY DIFFRACTIONx_scangle_it2.5472.5
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.0160.02
X-RAY DIFFRACTIONx_angle_d0.0540.05
X-RAY DIFFRACTIONx_planar_d0.0460.05
X-RAY DIFFRACTIONx_plane_restr0.0130.02
X-RAY DIFFRACTIONx_chiral_restr0.1750.15

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