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- PDB-3g7w: Islet Amyloid Polypeptide (IAPP or Amylin) Residues 1 to 22 fused... -

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Basic information

Entry
Database: PDB / ID: 3g7w
TitleIslet Amyloid Polypeptide (IAPP or Amylin) Residues 1 to 22 fused to Maltose Binding Protein
ComponentsMaltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein
KeywordsSugar binding protein / Hormone / native fold for amyloidogenic protein / Sugar transport / Transport / Amidation / Amyloid / Cleavage on pair of basic residues / 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 / detection of maltose stimulus / maltose transport complex ...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 / detection of maltose stimulus / maltose transport complex / negative regulation of osteoclast differentiation / Regulation of gene expression in beta cells / carbohydrate transport / positive regulation of cAMP/PKA signal transduction / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / bone resorption / negative regulation of protein-containing complex assembly / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / sensory perception of pain / positive regulation of calcium-mediated signaling / ATP-binding cassette (ABC) transporter complex / osteoclast differentiation / cell chemotaxis / hormone activity / cell-cell signaling / amyloid-beta binding / outer membrane-bounded periplasmic space / G alpha (s) signalling events / periplasmic space / positive regulation of MAPK cascade / positive regulation of apoptotic process / Amyloid fiber formation / receptor ligand activity / signaling receptor binding / neuronal cell body / lipid binding / apoptotic process / DNA damage response / signal transduction / extracellular space / extracellular region / identical protein binding / membrane
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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site ...Islet amyloid polypeptide / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltotriose / Maltose/maltodextrin-binding periplasmic protein / Islet amyloid polypeptide
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsWiltzius, J.J.W. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Protein Sci. / Year: 2009
Title: Atomic structures of IAPP (amylin) fusions suggest a mechanism for fibrillation and the role of insulin in the process
Authors: Wiltzius, J.J. / Sievers, S.A. / Sawaya, M.R. / Eisenberg, D.
History
DepositionFeb 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,53924
Polymers42,9301
Non-polymers2,61023
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Maltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein
hetero molecules

A: Maltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,07948
Polymers85,8592
Non-polymers5,22046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10190 Å2
ΔGint-456 kcal/mol
Surface area33500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.495, 84.495, 144.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Maltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein / MMBP / Maltodextrin-binding protein / Amylin / Diabetes-associated peptide / DAP / Insulinoma amyloid peptide


Mass: 42929.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, IAPP / Plasmid: pMal-a1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P10997
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0 M Ammonium Sulfate, 0.1M Sodium Acetate 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-C / Wavelength: 0.98085 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98085 Å / Relative weight: 1
ReflectionResolution: 1.75→90 Å / Num. obs: 53547 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.099 / Χ2: 1.038 / Net I/σ(I): 16.958
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.89120.431105470.8071100
1.89-2.0712.60.218105561.1471100
2.07-2.3812.60.153106231.0361100
2.38-2.9912.60.125107401.0711100
2.99-9011.80.097110811.117199

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å55.2 Å
Translation2.5 Å55.2 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0070refinement
PDB_EXTRACT3.006data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MPD

1mpd


Resolution: 1.75→55.22 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.183 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.895 / SU B: 3.691 / SU ML: 0.057 / SU R Cruickshank DPI: 0.095 / SU Rfree: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2720 5.1 %RANDOM
Rwork0.17 ---
obs0.171 53487 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.44 Å2 / Biso mean: 23.421 Å2 / Biso min: 11.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.71 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.75→55.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 146 366 3536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223267
X-RAY DIFFRACTIONr_bond_other_d0.0010.022130
X-RAY DIFFRACTIONr_angle_refined_deg1.1932.0014461
X-RAY DIFFRACTIONr_angle_other_deg0.8633.0015252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1235406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88225.87138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.29215525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.965157
X-RAY DIFFRACTIONr_chiral_restr0.0740.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02594
X-RAY DIFFRACTIONr_mcbond_it1.66621978
X-RAY DIFFRACTIONr_mcbond_other0.5182800
X-RAY DIFFRACTIONr_mcangle_it2.60233172
X-RAY DIFFRACTIONr_scbond_it2.21721289
X-RAY DIFFRACTIONr_scangle_it3.48731282
LS refinement shellResolution: 1.75→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 181 -
Rwork0.24 3616 -
all-3797 -
obs--97.63 %
Refinement TLS params.Method: refined / Origin x: -27.9287 Å / Origin y: -2.2304 Å / Origin z: -20.6772 Å
111213212223313233
T0.0215 Å2-0.0062 Å20.0009 Å2-0.0493 Å20.0159 Å2--0.0094 Å2
L0.5323 °2-0.2099 °20.0103 °2-0.6084 °2-0.2908 °2--0.7117 °2
S0.0368 Å °0.0635 Å °0.0456 Å °-0.0151 Å °-0.0122 Å °-0.0285 Å °0.0011 Å °0.0145 Å °-0.0245 Å °

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