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- PDB-7bg0: Fusion of MBP and the backbone of the long-acting amylin analog AM833. -

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Basic information

Entry
Database: PDB / ID: 7bg0
TitleFusion of MBP and the backbone of the long-acting amylin analog AM833.
ComponentsMaltose/maltodextrin-binding periplasmic protein,Islet amyloid polypeptide
KeywordsHORMONE / Amylin / AM833 / cagrilintide
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 / receptor ligand activity / Amyloid fiber formation / signaling receptor binding / neuronal cell body / apoptotic process / DNA damage response / lipid binding / 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsJohansson, E.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Development of Cagrilintide, a Long-Acting Amylin Analogue.
Authors: Kruse, T. / Hansen, J.L. / Dahl, K. / Schaffer, L. / Sensfuss, U. / Poulsen, C. / Schlein, M. / Hansen, A.M.K. / Jeppesen, C.B. / Dornonville de la Cour, C. / Clausen, T.R. / Johansson, E. / ...Authors: Kruse, T. / Hansen, J.L. / Dahl, K. / Schaffer, L. / Sensfuss, U. / Poulsen, C. / Schlein, M. / Hansen, A.M.K. / Jeppesen, C.B. / Dornonville de la Cour, C. / Clausen, T.R. / Johansson, E. / Fulle, S. / Skyggebjerg, R.B. / Raun, K.
History
DepositionJan 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Islet amyloid polypeptide
B: Maltose/maltodextrin-binding periplasmic protein,Islet amyloid polypeptide
D: Maltose/maltodextrin-binding periplasmic protein,Islet amyloid polypeptide
E: Maltose/maltodextrin-binding periplasmic protein,Islet amyloid polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,6666
Polymers177,9814
Non-polymers6852
Water00
1
A: Maltose/maltodextrin-binding periplasmic protein,Islet amyloid polypeptide
B: Maltose/maltodextrin-binding periplasmic protein,Islet amyloid polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3333
Polymers88,9912
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Maltose/maltodextrin-binding periplasmic protein,Islet amyloid polypeptide
E: Maltose/maltodextrin-binding periplasmic protein,Islet amyloid polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3333
Polymers88,9912
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.135, 179.135, 150.208
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 400)
d_2ens_1(chain "D" and resid 1 through 400)
d_1ens_2(chain "B" and (resid 1 through 366 or resid 501))
d_2ens_2chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSTHRA1 - 400
d_21ens_1LYSTHRF1 - 400
d_11ens_2LYSTHRB1 - 366
d_12ens_2MALMALC
d_21ens_2LYSTHRD1 - 366
d_22ens_2MALMALE

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.595912541962, -0.802961157519, 0.0119004978165), (-0.802987466286, 0.59598515094, 0.00358173800765), (-0.00996851648401, -0.00742154798846, -0.99992277167)-0.461060401563, -0.0163774043324, 130.083205304
2given(-0.593880596014, -0.804440822362, 0.0134462260714), (-0.804499631399, 0.593950960709, 0.00161225069361), (-0.00928335916682, -0.00985999951527, -0.999908295621)-0.406363318492, 0.0851006892836, 130.090527667

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Components

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


Mass: 44495.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, IAPP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9, UniProt: P10997
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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
Has ligand of interestN
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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20mM Tris pH 7.4, 50mM NaCl, 0.02 M magnesium chloride, 0.1 M HEPES pH 7.5, 22 %(w/v) polyacrylic acid 5100 sodium salt

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.89→37.55 Å / Num. obs: 40035 / % possible obs: 99.77 % / Redundancy: 5.7 % / Biso Wilson estimate: 63.76 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.09446 / Rpim(I) all: 0.04386 / Rrim(I) all: 0.1042 / Net I/σ(I): 16.7
Reflection shellResolution: 2.895→2.998 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.5807 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 3961 / CC1/2: 0.887 / CC star: 0.969 / Rpim(I) all: 0.2675 / Rrim(I) all: 0.6397 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G7V

3g7v


Resolution: 2.89→37.55 Å / SU ML: 0.4209 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.0437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.279 3970 4.99 %
Rwork0.2198 75638 -
obs0.2227 39962 99.41 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.32 Å2
Refinement stepCycle: LAST / Resolution: 2.89→37.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11887 0 46 0 11933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003712223
X-RAY DIFFRACTIONf_angle_d0.678116612
X-RAY DIFFRACTIONf_chiral_restr0.04371823
X-RAY DIFFRACTIONf_plane_restr0.00542152
X-RAY DIFFRACTIONf_dihedral_angle_d5.08551647
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONcartesian NCS0.757574847231
ens_2d_2BX-RAY DIFFRACTIONcartesian NCS0.84854340208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.930.3291400.28752572X-RAY DIFFRACTION96.86
2.93-2.970.34461440.28132718X-RAY DIFFRACTION100
2.97-3.010.34531460.26822758X-RAY DIFFRACTION100
3.01-3.050.29311400.26142726X-RAY DIFFRACTION100
3.05-3.090.33651440.29972748X-RAY DIFFRACTION100
3.09-3.140.35991400.29722692X-RAY DIFFRACTION100
3.14-3.190.41211390.35782722X-RAY DIFFRACTION99.69
3.19-3.240.38141340.32322499X-RAY DIFFRACTION93.9
3.24-3.290.3961360.34342629X-RAY DIFFRACTION96.01
3.29-3.350.47131460.29992690X-RAY DIFFRACTION99.86
3.35-3.420.28681440.27312763X-RAY DIFFRACTION99.97
3.42-3.490.31731440.25422725X-RAY DIFFRACTION99.9
3.49-3.560.32441440.26842727X-RAY DIFFRACTION99.97
3.56-3.650.33291360.25352686X-RAY DIFFRACTION99.86
3.65-3.740.32451420.23472716X-RAY DIFFRACTION99.86
3.74-3.840.39941480.21782703X-RAY DIFFRACTION99.89
3.84-3.950.29131440.22192729X-RAY DIFFRACTION99.76
3.95-4.080.32641400.21532709X-RAY DIFFRACTION99.89
4.08-4.220.24171460.20322696X-RAY DIFFRACTION99.72
4.22-4.390.23931440.192726X-RAY DIFFRACTION100
4.39-4.590.23921380.20192736X-RAY DIFFRACTION99.72
4.59-4.830.24311450.17872694X-RAY DIFFRACTION99.82
4.84-5.140.22151440.18032717X-RAY DIFFRACTION100
5.14-5.530.26411380.20412736X-RAY DIFFRACTION100
5.53-6.090.2571420.2132707X-RAY DIFFRACTION99.96
6.09-6.970.24451460.19142680X-RAY DIFFRACTION100
6.97-8.750.17351360.16342742X-RAY DIFFRACTION100
8.76-41.360.19581400.15212692X-RAY DIFFRACTION98.61

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