[English] 日本語
Yorodumi
- PDB-3fr1: NFLVHS segment from Islet Amyloid Polypeptide (IAPP or Amylin) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fr1
TitleNFLVHS segment from Islet Amyloid Polypeptide (IAPP or Amylin)
ComponentsIslet amyloid polypeptideAmylin
KeywordsPROTEIN FIBRIL / amyloid-like protofibril / Amidation / Amyloid / Cleavage on pair of basic residues / Hormone / Polymorphism / Secreted
Function / homology
Function and homology information


: / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly ...: / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly / positive regulation of cAMP-mediated signaling / positive regulation of calcium-mediated signaling / bone resorption / sensory perception of pain / osteoclast differentiation / hormone activity / cell-cell signaling / amyloid-beta binding / G alpha (s) signalling events / positive regulation of MAPK cascade / receptor ligand activity / positive regulation of apoptotic process / Amyloid fiber formation / signaling receptor binding / lipid binding / apoptotic process / signal transduction / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Islet amyloid polypeptide / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family
Similarity search - Domain/homology
Islet amyloid polypeptide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsWiltzius, J.J.W. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Molecular mechanisms for protein-encoded inheritance
Authors: Wiltzius, J.J. / Landau, M. / Nelson, R. / Sawaya, M.R. / Apostol, M.I. / Goldschmidt, L. / Soriaga, A.B. / Cascio, D. / Rajashankar, K. / Eisenberg, D.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Islet amyloid polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7522
Polymers7171
Non-polymers351
Water181
1
A: Islet amyloid polypeptide
hetero molecules

A: Islet amyloid polypeptide
hetero molecules


  • defined by author
  • 1.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)1,5054
Polymers1,4342
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
2
A: Islet amyloid polypeptide
hetero molecules

A: Islet amyloid polypeptide
hetero molecules


  • defined by author
  • 1.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)1,5054
Polymers1,4342
Non-polymers712
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)11.480, 9.552, 38.582
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE BIOLOGICAL UNIT IS A PAIR OF BETA SHEETS. ONE SHEET IS CONSTRUCTED FROM CHAIN A AND A CRYSTALLOGRAPHIC SYMMETRY OPERATOR (I.E. X,Y,Z AND -X,1/2+Y,-1/2-Z). THE SECOND SHEET IS CONSTRUCTED FROM X+1,Y,Z AND 1-X,1/2+Y,-1/2-Z.

-
Components

#1: Protein/peptide Islet amyloid polypeptide / Amylin / Amylin / Diabetes-associated peptide / DAP / Insulinoma amyloid peptide


Mass: 716.805 Da / Num. of mol.: 1 / Fragment: sequence database residues 47-52 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10997
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.475554 Å3/Da / Density % sol: 16.641487 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.18M MgCl2, 0.09M HEPES pH 7.5, 27% isopropanol, and 10% glycerol, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→90 Å / Num. all: 434 / Num. obs: 434 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.183 / Χ2: 0.992
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.996.20.419680.70582.9
1.99-2.195.80.258851.02897.7
2.19-2.515.10.292861.0792.5
2.51-3.165.60.171881.04897.8
3.16-904.60.1381071.08897.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.838 / SU B: 3.496 / SU ML: 0.1 / SU R Cruickshank DPI: 0.216 / SU Rfree: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 43 10.2 %RANDOM
Rwork0.192 ---
obs0.196 422 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.65 Å2 / Biso mean: 14.911 Å2 / Biso min: 7.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2---1.19 Å20 Å2
3---2.27 Å2
Refinement stepCycle: LAST / Resolution: 1.85→11 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms51 0 1 1 53
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02152
X-RAY DIFFRACTIONr_bond_other_d0.0010.0230
X-RAY DIFFRACTIONr_angle_refined_deg0.6081.88970
X-RAY DIFFRACTIONr_angle_other_deg0.546373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.80555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.51623.3333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.831157
X-RAY DIFFRACTIONr_chiral_restr0.0460.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0256
X-RAY DIFFRACTIONr_gen_planes_other00.0212
X-RAY DIFFRACTIONr_mcbond_it1.476230
X-RAY DIFFRACTIONr_mcbond_other0.369211
X-RAY DIFFRACTIONr_mcangle_it2.491348
X-RAY DIFFRACTIONr_scbond_it1.299222
X-RAY DIFFRACTIONr_scangle_it2.051322
LS refinement shellResolution: 1.85→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 4 -
Rwork0.295 24 -
all-28 -
obs--75.68 %

+
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