[English] 日本語
Yorodumi
- PDB-4p65: Crystal structure of an cyclohexylalanine substituted insulin analog. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p65
TitleCrystal structure of an cyclohexylalanine substituted insulin analog.
Components(Insulin) x 2
KeywordsHORMONE / protein hormone / non-standard mutagenesis
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / positive regulation of protein autophosphorylation / 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 / positive regulation of glycogen biosynthetic process / negative regulation of gluconeogenesis / Signal attenuation / fatty acid homeostasis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of insulin receptor signaling pathway / 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 / activation of protein kinase B activity / transport vesicle / nitric oxide-cGMP-mediated signaling / COPI-mediated anterograde transport / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of nitric-oxide synthase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / positive regulation of glycolytic process / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / endosome lumen / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of cell differentiation / Regulation of insulin secretion / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / positive regulation of neuron projection development / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / cognition / glucose metabolic process / vasodilation / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / positive regulation of cell growth / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPandyarajan, V. / Wan, Z. / Weiss, M.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Aromatic Anchor at an Invariant Hormone-Receptor Interface: FUNCTION OF INSULIN RESIDUE B24 WITH APPLICATION TO PROTEIN DESIGN.
Authors: Pandyarajan, V. / Smith, B.J. / Phillips, N.B. / Whittaker, L. / Cox, G.P. / Wickramasinghe, N. / Menting, J.G. / Wan, Z.L. / Whittaker, J. / Ismail-Beigi, F. / Lawrence, M.C. / Weiss, M.A.
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_oper_list / pdbx_validate_symm_contact / refine_hist / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin
B: Insulin
C: Insulin
D: Insulin
E: Insulin
F: Insulin
G: Insulin
H: Insulin
I: Insulin
J: Insulin
K: Insulin
L: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,61822
Polymers34,85212
Non-polymers76610
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18580 Å2
ΔGint-233 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.040, 60.900, 59.300
Angle α, β, γ (deg.)90.00, 112.25, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
Insulin


Mass: 2383.698 Da / Num. of mol.: 6 / Fragment: UNP residues 90-110 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide
Insulin


Mass: 3424.967 Da / Num. of mol.: 6 / Fragment: UNP residues 25-54 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308

-
Non-polymers , 4 types, 217 molecules

#3: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 6 / 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.: 207 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: sodium citrate, phenol, sodium chloride, zinc acetate, tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→42.3 Å / Num. obs: 54128 / % possible obs: 95.8 % / Redundancy: 1.9 % / Net I/σ(I): 13.9
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.6 / % possible all: 99.3

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZNJ

1znj


Resolution: 1.5→42.3 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 4823 10.01 %random selection
Rwork0.1598 ---
obs0.1641 48189 99.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 46 207 2574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012620
X-RAY DIFFRACTIONf_angle_d1.3513522
X-RAY DIFFRACTIONf_dihedral_angle_d14.777980
X-RAY DIFFRACTIONf_chiral_restr0.065383
X-RAY DIFFRACTIONf_plane_restr0.006445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.36171660.33191447X-RAY DIFFRACTION99
1.5171-1.53490.34971600.30431471X-RAY DIFFRACTION100
1.5349-1.55360.2911580.27341420X-RAY DIFFRACTION99
1.5536-1.57330.31111600.26441445X-RAY DIFFRACTION99
1.5733-1.5940.29981660.24371436X-RAY DIFFRACTION100
1.594-1.61580.27211560.22971446X-RAY DIFFRACTION100
1.6158-1.63890.25411590.2161465X-RAY DIFFRACTION100
1.6389-1.66340.23831610.20061417X-RAY DIFFRACTION100
1.6634-1.68940.23991620.17671456X-RAY DIFFRACTION100
1.6894-1.71710.21561700.17991435X-RAY DIFFRACTION100
1.7171-1.74670.22541880.17281423X-RAY DIFFRACTION100
1.7467-1.77840.24551630.1681487X-RAY DIFFRACTION100
1.7784-1.81270.2151540.16831435X-RAY DIFFRACTION100
1.8127-1.84970.22821550.1581466X-RAY DIFFRACTION100
1.8497-1.88990.22331550.15811435X-RAY DIFFRACTION100
1.8899-1.93380.23661710.15611464X-RAY DIFFRACTION100
1.9338-1.98220.20371600.1541456X-RAY DIFFRACTION100
1.9822-2.03580.18221650.14911436X-RAY DIFFRACTION100
2.0358-2.09570.18511720.14041444X-RAY DIFFRACTION100
2.0957-2.16330.19081590.14551452X-RAY DIFFRACTION100
2.1633-2.24060.18531620.1411459X-RAY DIFFRACTION100
2.2406-2.33040.19691540.14341456X-RAY DIFFRACTION100
2.3304-2.43640.19791580.15131481X-RAY DIFFRACTION100
2.4364-2.56480.18171840.13941434X-RAY DIFFRACTION100
2.5648-2.72550.20341340.15281490X-RAY DIFFRACTION100
2.7255-2.93590.19631480.15951466X-RAY DIFFRACTION100
2.9359-3.23130.19671690.16041449X-RAY DIFFRACTION100
3.2313-3.69860.17941580.15091480X-RAY DIFFRACTION99
3.6986-4.65890.1861510.14171439X-RAY DIFFRACTION97
4.6589-42.31630.21241450.17421276X-RAY DIFFRACTION85

+
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