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- PDB-3ftl: NVGSNTY segment from Islet Amyloid Polypeptide (IAPP or Amylin), ... -

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Basic information

Entry
Database: PDB / ID: 3ftl
TitleNVGSNTY segment from Islet Amyloid Polypeptide (IAPP or Amylin), dehydrated crystal form
ComponentsNVGSNTY heptapeptide segment from Islet Amyloid Polypeptide
KeywordsPROTEIN FIBRIL / amyloid-like protofibril / MEMBRANE PROTEIN
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: 1.6 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 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide
B: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide


Theoretical massNumber of molelcules
Total (without water)1,5082
Polymers1,5082
Non-polymers00
Water543
1
A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide
B: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide

A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide
B: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide

A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide
B: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide


Theoretical massNumber of molelcules
Total (without water)4,5236
Polymers4,5236
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_545x,y-1,z1
2
A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide
B: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide

A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide
B: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide

A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide
B: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide


Theoretical massNumber of molelcules
Total (without water)4,5236
Polymers4,5236
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_555-x,y+1/2,-z1
crystal symmetry operation2_565-x,y+3/2,-z1
crystal symmetry operation2_545-x,y-1/2,-z1
3
A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide


  • defined by software
  • 754 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)7541
Polymers7541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide


Theoretical massNumber of molelcules
Total (without water)7541
Polymers7541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.653, 4.824, 29.048
Angle α, β, γ (deg.)90.000, 101.020, 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 CHAIN A AND CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE "B" CELL DIMENSION (E.G. X,Y,Z AND X,Y+1,Z). THE SECOND SHEET IS CONSTRUCTED FROM 1-X, Y+1/2,1-Z AND CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE "B" CELL DIMENSION (E.G. 1-X, Y+3/2,1-Z). A SECOND BIOLOGICAL UNIT, SIMILAR TO THE FIRST, IS AN INDEFINITELY LONG PAIR OF SHEETS. ONE SHEET FORMED BY CHAIN B AND CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE "B" CELL DIMENSION (E.G. X,Y,Z AND X,Y+1,Z). THE SECOND SHEET IS CONSTRUCTED FROM -X, Y+1/2,-Z AND CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE "B" CELL DIMENSION (E.G. -X, Y+3/2,-Z).

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Components

#1: Protein/peptide NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide


Mass: 753.759 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10997*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 25% PEG 3350, 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, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→90 Å / Num. all: 1103 / Num. obs: 1103 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.155 / Χ2: 1.005
Reflection shellResolution: 1.6→1.72 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / Num. unique all: 187 / Χ2: 1.045 / % possible all: 94

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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
Starting model: PDB entry 3FTK

3ftk


Resolution: 1.6→28.51 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.155 / WRfactor Rwork: 0.117 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.907 / SU B: 1.143 / SU ML: 0.039 / SU R Cruickshank DPI: 0.093 / SU Rfree: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.158 119 10.8 %RANDOM
Rwork0.124 ---
obs0.127 1103 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 40.33 Å2 / Biso mean: 2.75 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms106 0 0 3 109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021106
X-RAY DIFFRACTIONr_bond_other_d0.0020.0256
X-RAY DIFFRACTIONr_angle_refined_deg1.661.919144
X-RAY DIFFRACTIONr_angle_other_deg2.423138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.079512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.00226.6676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.5681512
X-RAY DIFFRACTIONr_chiral_restr0.10.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02124
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0220
X-RAY DIFFRACTIONr_mcbond_it0.681.568
X-RAY DIFFRACTIONr_mcbond_other0.0331.528
X-RAY DIFFRACTIONr_mcangle_it0.8852108
X-RAY DIFFRACTIONr_scbond_it0.646338
X-RAY DIFFRACTIONr_scangle_it0.7214.536
LS refinement shellResolution: 1.6→1.784 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.231 29 -
Rwork0.178 239 -
all-268 -
obs--93.06 %

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