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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fth
TitleNFLVHSS segment from Islet Amyloid Polypeptide (IAPP or Amylin)
ComponentsNFLVHSS heptapeptide from Islet Amyloid Polypeptide
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
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 / positive regulation of protein kinase A signaling / negative regulation of osteoclast differentiation / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly / bone resorption ...amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / positive regulation of protein kinase A signaling / negative regulation of osteoclast differentiation / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly / bone resorption / sensory perception of pain / positive regulation of calcium-mediated signaling / 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: 1.84 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 13, 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: NFLVHSS heptapeptide from Islet Amyloid Polypeptide
B: NFLVHSS heptapeptide from Islet Amyloid Polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7043
Polymers1,6082
Non-polymers961
Water1086
1
A: NFLVHSS heptapeptide from Islet Amyloid Polypeptide
hetero molecules

B: NFLVHSS heptapeptide from Islet Amyloid Polypeptide


Theoretical massNumber of molelcules
Total (without water)1,7043
Polymers1,6082
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area660 Å2
ΔGint-10 kcal/mol
Surface area1660 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-8 kcal/mol
Surface area1660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)9.725, 21.600, 26.086
Angle α, β, γ (deg.)90.000, 95.560, 90.000
Int Tables number4
Space group name H-MP1211
DetailsTHE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS A INDEFINITELY LONG PAIR OF SHEETS (A PROTOFIBRIL). ONE SHEET FORMED BY CHAINS A AND B AND THEIR CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE "A" CELL DIMENSION (E.G. X,Y,Z AND X+1,Y,Z). THE SECOND SHEET IS CONSTRUCTED FROM -X, Y+1/2,-Z AND THEIR CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE "A" CELL DIMENSION (E.G. -X+1, Y+1/2,-Z).

-
Components

#1: Protein/peptide NFLVHSS heptapeptide from Islet Amyloid Polypeptide


Mass: 803.883 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10997*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.7 Å3/Da / Density % sol: 27.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.5M Ammonium Sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 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: Nov 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. all: 932 / Num. obs: 932 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.189 / Χ2: 1.054
Reflection shellResolution: 1.8→1.94 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / Num. unique all: 180 / Χ2: 1.122 / % possible all: 89.1

-
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: 1.84→16.6 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.29 / WRfactor Rwork: 0.235 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.837 / SU B: 3.396 / SU ML: 0.108 / SU R Cruickshank DPI: 0.318 / SU Rfree: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 101 10.9 %RANDOM
Rwork0.238 ---
obs0.242 926 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 38.59 Å2 / Biso mean: 8.193 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.1 Å2
2--0.71 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.84→16.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms124 0 5 7 136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021132
X-RAY DIFFRACTIONr_bond_other_d0.0010.0276
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.981182
X-RAY DIFFRACTIONr_angle_other_deg1.1653190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.686516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.22523.3336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6711520
X-RAY DIFFRACTIONr_chiral_restr0.1120.222
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0228
X-RAY DIFFRACTIONr_mcbond_it2.18276
X-RAY DIFFRACTIONr_mcbond_other0.581228
X-RAY DIFFRACTIONr_mcangle_it3.2463124
X-RAY DIFFRACTIONr_scbond_it2.367256
X-RAY DIFFRACTIONr_scangle_it3.044356
LS refinement shellResolution: 1.84→1.892 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 5 -
Rwork0.255 64 -
all-69 -
obs--89.61 %

+
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