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

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Basic information

Entry
Database: PDB / ID: 3ftk
TitleNVGSNTY segment from Islet Amyloid Polypeptide (IAPP or Amylin), hydrated crystal form
ComponentsNVGSNTY heptapeptide segment 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: 1.5 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 / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)7541
Polymers7541
Non-polymers00
Water905
1
A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide

A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide

A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide


Theoretical massNumber of molelcules
Total (without water)2,2613
Polymers2,2613
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

A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide

A: NVGSNTY heptapeptide segment from Islet Amyloid Polypeptide


Theoretical massNumber of molelcules
Total (without water)2,2613
Polymers2,2613
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


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)20.630, 4.700, 21.009
Angle α, β, γ (deg.)90.000, 92.280, 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 -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.: 1 / 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.: 5 / 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: Oct 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→90 Å / Num. all: 742 / Num. obs: 742 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.189 / Χ2: 1.033
Reflection shellResolution: 1.5→1.62 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.2 / Num. unique all: 134 / Χ2: 1.191 / % possible all: 86.5

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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: 1.5→20.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.158 / WRfactor Rwork: 0.151 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.919 / SU B: 1.176 / SU ML: 0.043 / SU R Cruickshank DPI: 0.086 / SU Rfree: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.158 77 10.4 %RANDOM
Rwork0.148 ---
obs0.149 739 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 10.79 Å2 / Biso mean: 4.184 Å2 / Biso min: 2.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å2-0.14 Å2
2--0.28 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.98 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms53 0 0 5 58
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02153
X-RAY DIFFRACTIONr_bond_other_d0.0020.0228
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.91972
X-RAY DIFFRACTIONr_angle_other_deg0.687369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg52.82526.6673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.731156
X-RAY DIFFRACTIONr_chiral_restr0.0520.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0262
X-RAY DIFFRACTIONr_gen_planes_other00.0210
X-RAY DIFFRACTIONr_mcbond_it0.4331.534
X-RAY DIFFRACTIONr_mcbond_other0.1011.514
X-RAY DIFFRACTIONr_mcangle_it0.645254
X-RAY DIFFRACTIONr_scbond_it0.618319
X-RAY DIFFRACTIONr_scangle_it1.0114.518
LS refinement shellResolution: 1.5→1.672 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.277 20 -
Rwork0.199 155 -
all-175 -
obs--84.95 %

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