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- PDB-3fth: NFLVHSS segment from Islet Amyloid Polypeptide (IAPP or Amylin) -

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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 / 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: 1.84 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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).

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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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2

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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

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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: 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

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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: 1.84→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 %

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