[English] 日本語
Yorodumi
- PDB-5mam: Human insulin in complex with serotonin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mam
TitleHuman insulin in complex with serotonin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / serotonin / complex / specificity
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 / 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 fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / 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 / alpha-beta T cell activation / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of dendritic spine maintenance / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / positive regulation of insulin receptor signaling pathway / negative regulation of respiratory burst involved in inflammatory response / 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 / 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 / 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 / acute-phase response / positive regulation of long-term synaptic potentiation / positive regulation of D-glucose import across plasma membrane / positive regulation of protein secretion / 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 / receptor ligand activity / 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: 2.2 Å
AuthorsBrzozowski, A.M. / Turkenburg, J.P. / Jiracek, J. / Zakova, L.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Computational and structural evidence for neurotransmitter-mediated modulation of the oligomeric states of human insulin in storage granules.
Authors: Palivec, V. / Viola, C.M. / Kozak, M. / Ganderton, T.R. / Krizkova, K. / Turkenburg, J.P. / Haluskova, P. / Zakova, L. / Jiracek, J. / Jungwirth, P. / Brzozowski, A.M.
History
DepositionNov 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
I: Insulin A chain
J: Insulin B chain
K: Insulin A chain
L: Insulin B chain
M: Insulin A chain
N: Insulin B chain
O: Insulin A chain
P: Insulin B chain
Q: Insulin A chain
R: Insulin B chain
S: Insulin A chain
T: Insulin B chain
U: Insulin A chain
V: Insulin B chain
W: Insulin A chain
X: Insulin B chain
Y: Insulin A chain
Z: Insulin B chain
0: Insulin A chain
1: Insulin B chain
2: Insulin A chain
3: Insulin B chain
4: Insulin A chain
5: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,35662
Polymers93,08232
Non-polymers3,27430
Water4,648258
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)36,04027
Polymers34,90612
Non-polymers1,13415
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area17210 Å2
ΔGint-334 kcal/mol
Surface area11550 Å2
MethodPISA
2
E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
I: Insulin A chain
J: Insulin B chain
K: Insulin A chain
L: Insulin B chain
M: Insulin A chain
N: Insulin B chain
O: Insulin A chain
P: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,16522
Polymers34,90612
Non-polymers1,25910
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19250 Å2
ΔGint-269 kcal/mol
Surface area11590 Å2
MethodPISA
3
Q: Insulin A chain
R: Insulin B chain
S: Insulin A chain
T: Insulin B chain
U: Insulin A chain
V: Insulin B chain
W: Insulin A chain
X: Insulin B chain
Y: Insulin A chain
Z: Insulin B chain
0: Insulin A chain
1: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,98921
Polymers34,90612
Non-polymers1,0839
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17950 Å2
ΔGint-271 kcal/mol
Surface area12080 Å2
MethodPISA
4
2: Insulin A chain
3: Insulin B chain
4: Insulin A chain
5: Insulin B chain
hetero molecules

2: Insulin A chain
3: Insulin B chain
4: Insulin A chain
5: Insulin B chain
hetero molecules

2: Insulin A chain
3: Insulin B chain
4: Insulin A chain
5: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,56830
Polymers34,90612
Non-polymers1,66218
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area20510 Å2
ΔGint-655 kcal/mol
Surface area9880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.960, 158.960, 76.530
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-101-

ZN

21B-102-

CL

31D-101-

ZN

41D-102-

CL

513-101-

ZN

615-101-

ZN

715-102-

CL

-
Components

-
Protein/peptide , 2 types, 32 molecules ACEGIKMOQSUWY024BDFHJLNPRTVXZ135

#1: Protein/peptide
Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide
Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308

-
Non-polymers , 4 types, 288 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H12N2O / Comment: neurotransmitter*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Zn-free human insulin was dissolved in 20 mM HCl at 5 mg/mL. The well solution contained 5 mM ZnAcetate, 35 mM NaCitrate, 1.1 M NaCl, 0.3M Tris pH 7.5, 40 mM serotonin. Hanging drops were ...Details: Zn-free human insulin was dissolved in 20 mM HCl at 5 mg/mL. The well solution contained 5 mM ZnAcetate, 35 mM NaCitrate, 1.1 M NaCl, 0.3M Tris pH 7.5, 40 mM serotonin. Hanging drops were set up in 1:1 protein:well volume ratios.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97631 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
ReflectionResolution: 2.2→51.18 Å / Num. obs: 36018 / % possible obs: 98.4 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.3
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.46 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→51.18 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.21 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.269 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28037 1786 5 %RANDOM
Rwork0.20201 ---
obs0.20593 34232 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.744 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.3 Å2-0 Å2
2---0.59 Å20 Å2
3---1.92 Å2
Refinement stepCycle: 1 / Resolution: 2.2→51.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5705 0 198 258 6161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196131
X-RAY DIFFRACTIONr_bond_other_d0.0030.025320
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9948330
X-RAY DIFFRACTIONr_angle_other_deg1.016312107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7035743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8223.566244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26115824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2261517
X-RAY DIFFRACTIONr_chiral_restr0.1010.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021535
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7154.4593051
X-RAY DIFFRACTIONr_mcbond_other3.7154.4573050
X-RAY DIFFRACTIONr_mcangle_it5.6676.6243767
X-RAY DIFFRACTIONr_mcangle_other5.6676.6253768
X-RAY DIFFRACTIONr_scbond_it4.0844.6343077
X-RAY DIFFRACTIONr_scbond_other4.0834.6343078
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7216.8624556
X-RAY DIFFRACTIONr_long_range_B_refined8.23250.9396973
X-RAY DIFFRACTIONr_long_range_B_other8.23150.9376974
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 143 -
Rwork0.304 2387 -
obs--94.16 %

+
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