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- PDB-3fr1: NFLVHS segment from Islet Amyloid Polypeptide (IAPP or Amylin) -

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Basic information

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


amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amylin receptor 1 signaling pathway / 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 / Regulation of gene expression in beta cells ...amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amylin receptor 1 signaling pathway / 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 / Regulation of gene expression in beta cells / positive regulation of cAMP/PKA signal transduction / bone resorption / negative regulation of protein-containing complex assembly / 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 / positive regulation of apoptotic process / receptor ligand activity / Amyloid fiber formation / signaling receptor binding / neuronal cell body / apoptotic process / lipid binding / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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Components

#1: Protein/peptide Islet amyloid polypeptide / 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


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


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

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Experimental details

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Experiment

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

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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

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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

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Phasing

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

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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 %

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