[English] 日本語
Yorodumi
- PDB-1lph: LYS(B28)PRO(B29)-HUMAN INSULIN -

+
Open data


ID or keywords:

Loading...

-
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 NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / 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 / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic 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 / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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 / Phenol


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

-
Details

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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more