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- PDB-3g7v: Islet Amyloid Polypeptide (IAPP or Amylin) fused to Maltose Bindi... -

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Basic information

Entry
Database: PDB / ID: 3g7v
TitleIslet Amyloid Polypeptide (IAPP or Amylin) 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 signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport ...: / 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 binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / 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 / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / osteoclast differentiation / hormone activity / cell-cell signaling / outer membrane-bounded periplasmic space / amyloid-beta binding / G alpha (s) signalling events / positive regulation of MAPK cascade / receptor ligand activity / periplasmic space / positive regulation of apoptotic process / Amyloid fiber formation / signaling receptor binding / lipid binding / apoptotic process / DNA damage response / signal transduction / extracellular space / extracellular region / membrane / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2190 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2190 / 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / Helix non-globular / Special / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / 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: 1.86 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 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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 / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)181,03928
Polymers177,7694
Non-polymers3,27124
Water15,529862
1
A: Maltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein
B: Maltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,51814
Polymers88,8842
Non-polymers1,63312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-88 kcal/mol
Surface area31310 Å2
MethodPISA
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C: Maltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein
D: Maltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,52214
Polymers88,8842
Non-polymers1,63712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-96 kcal/mol
Surface area31310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.025, 96.407, 103.996
Angle α, β, γ (deg.)90.000, 90.530, 90.000
Int Tables number4
Space group name H-MP1211

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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: 44442.172 Da / Num. of mol.: 4
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 / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 862 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
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: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→90 Å / Num. all: 169517 / Num. obs: 169517 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.09 / Net I/σ(I): 27.432
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.925.20.46165921.101196.9
1.92-1.995.20.287166701.09196.9
1.99-2.085.30.202167001.096197.4
2.08-2.195.30.135168261.055198
2.19-2.335.40.101168840.96198.3
2.33-2.515.60.079169830.983198.8
2.51-2.765.70.062170681.034199
2.76-3.165.70.053171171.102199.3
3.16-3.995.70.045172311.325199.5
3.99-905.60.035174461.142199.6

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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
REFMAC5.5.0070refinement
PDB_EXTRACT3.006data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MPD

1mpd


Resolution: 1.86→73.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.887 / SU B: 4.943 / SU ML: 0.071 / SU R Cruickshank DPI: 0.118 / SU Rfree: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 8507 5 %RANDOM
Rwork0.176 ---
obs0.178 169484 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.31 Å2 / Biso mean: 20.269 Å2 / Biso min: 6.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.03 Å2
2---0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.86→73.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12244 0 197 862 13303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212779
X-RAY DIFFRACTIONr_bond_other_d0.0010.028467
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.97217377
X-RAY DIFFRACTIONr_angle_other_deg1.125320823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.33251606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22625.876548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41152083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8151525
X-RAY DIFFRACTIONr_chiral_restr0.0990.21917
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022386
X-RAY DIFFRACTIONr_mcbond_it1.93827950
X-RAY DIFFRACTIONr_mcbond_other0.62123226
X-RAY DIFFRACTIONr_mcangle_it2.912312723
X-RAY DIFFRACTIONr_scbond_it2.46524825
X-RAY DIFFRACTIONr_scangle_it3.71334646
LS refinement shellResolution: 1.86→1.905 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 565 -
Rwork0.226 10893 -
all-11458 -
obs--90.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7020.04310.1311.1782-0.32471.0876-0.00350.10160.0125-0.1942-0.0339-0.05960.14470.05780.03740.05070.02310.01120.04080.01490.037682.104617.839439.3243
20.70470.1432-0.10961.01740.12610.91130.0430.08340.0197-0.0875-0.0226-0.0359-0.0469-0.0158-0.02040.02580.0267-0.0050.04-0.00040.0336125.8542.011342.8313
30.9491-0.1466-0.11021.0295-0.13990.6805-0.02190.017-0.04620.0349-0.0150.08480.0098-0.07080.03680.05980.0004-0.00530.0485-0.02640.022142.703943.001422.1592
41.14210.37730.12551.2421-0.04220.68990.0401-0.06380.15350.0534-0.03630.20020.0159-0.0866-0.00380.0552-0.01670.00860.0469-0.0250.049239.567727.1478-21.6199
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 398
2X-RAY DIFFRACTION2B1 - 398
3X-RAY DIFFRACTION3C1 - 397
4X-RAY DIFFRACTION4D1 - 397

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