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- PDB-4mvk: Crystal structure of an engineered lipocalin (Anticalin US7) in c... -

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Basic information

Entry
Database: PDB / ID: 4mvk
TitleCrystal structure of an engineered lipocalin (Anticalin US7) in complex with the Alzheimer amyloid peptide fragment VFFAED
Components
  • Amyloid peptide fragment VFFAED
  • Neutrophil gelatinase-associated lipocalin
KeywordsPROTEIN BINDING/PROTEIN FIBRIL / beta-barrel / engineered lipocalin / binding protein / PROTEIN BINDING-PROTEIN FIBRIL complex
Function / homology
Function and homology information


positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / response to mycotoxin / response to blue light ...positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / response to mycotoxin / response to blue light / cellular response to increased oxygen levels / response to fructose / cellular response to X-ray / short-term memory / amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / cellular response to interleukin-6 / iron ion sequestering activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / enterobactin binding / regulation of synapse structure or activity / axon midline choice point recognition / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / response to herbicide / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Lysosome Vesicle Biogenesis / astrocyte projection / response to iron(II) ion / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / positive regulation of reactive oxygen species biosynthetic process / dendrite development / positive regulation of protein metabolic process / TRAF6 mediated NF-kB activation / signaling receptor activator activity / Advanced glycosylation endproduct receptor signaling / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / transition metal ion binding / main axon / regulation of multicellular organism growth / cellular response to interleukin-1 / intracellular copper ion homeostasis / ECM proteoglycans / regulation of presynapse assembly / long-term memory / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / cellular response to nutrient levels / positive regulation of chemokine production / cellular response to manganese ion / Notch signaling pathway / clathrin-coated pit / extrinsic apoptotic signaling pathway in absence of ligand / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / positive regulation of endothelial cell migration / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / positive regulation of interleukin-1 beta production / adult locomotory behavior / endosome lumen / dendritic shaft / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / acute-phase response / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / microglial cell activation / serine-type endopeptidase inhibitor activity
Similarity search - Function
Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Lipocalin family conserved site / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / PH-like domain superfamily / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsEichinger, A. / Skerra, A.
CitationJournal: Biochem.J. / Year: 2016
Title: High-affinity Anticalins with aggregation-blocking activity directed against the Alzheimer beta-amyloid peptide.
Authors: Rauth, S. / Hinz, D. / Borger, M. / Uhrig, M. / Mayhaus, M. / Riemenschneider, M. / Skerra, A.
History
DepositionSep 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
B: Amyloid peptide fragment VFFAED


Theoretical massNumber of molelcules
Total (without water)22,2842
Polymers22,2842
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-5 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.970, 59.230, 61.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / ...NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / Siderocalin LCN2 / p25


Mass: 21533.420 Da / Num. of mol.: 1 / Fragment: UNP residues 21-198
Mutation: Q28H,L36V,A40K,I41S,Q49W,L70G,R72G,K73T,D77H,W79K,C87S,N96R,Y100R,L103R,Y106A,K125V,S127Q,Y132S,K134N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: engineered variant US7, HNL, LCN2, LCN2 (NGAL_HUMAN), NGAL
Plasmid: pNGAL98-US7 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1(F-) / References: UniProt: P80188
#2: Protein/peptide Amyloid peptide fragment VFFAED


Mass: 750.819 Da / Num. of mol.: 1 / Fragment: UNP residues 689-694 / Source method: obtained synthetically
Details: The Abeta hexapeptide fragment VFFAED was synthesized with an acetylated N- and an amidated C-terminus.
Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 27 % (w/v) PEG 8000, 100 mM MES, pH 6.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 18, 2010 / Details: mirrors
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.5→42.571 Å / Num. all: 30318 / Num. obs: 30318 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.078 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.5870.34823059943570.348100
1.58-1.687.10.2452.92925341400.245100
1.68-1.797.10.1684.12775838850.168100
1.79-1.947.20.1414.42631136440.141100
1.94-2.127.20.115.82442433750.11100
2.12-2.377.20.0877.32210130530.087100
2.37-2.747.20.06991958827090.069100
2.74-3.357.20.0787.21662623200.078100
3.35-4.746.90.05810.71266918310.05899.5
4.74-26.666.10.03318.9616910040.03394.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.71 Å26.66 Å
Translation1.71 Å26.66 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L6M

1l6m


Resolution: 1.5→42.57 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1959 / WRfactor Rwork: 0.1728 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9001 / SU B: 2.254 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0677 / SU Rfree: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 1530 5.1 %RANDOM
Rwork0.1654 ---
all0.1664 30318 --
obs0.1654 30226 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.46 Å2 / Biso mean: 24.3619 Å2 / Biso min: 8.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å2-0 Å2-0 Å2
2---0.26 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 0 157 1598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021477
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.951995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0785175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7123.80371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33715256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.517159
X-RAY DIFFRACTIONr_chiral_restr0.1780.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211124
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 110 -
Rwork0.239 1915 -
all-2025 -
obs--99.7 %
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)
11.29820.1708-0.19021.45360.08921.532-0.01750.05550.0118-0.084-0.00370.0771-0.0439-0.00350.02120.025-0.0024-0.00560.01370.00190.0046-19.1707-2.50847.9208
25.3023-1.3949-4.40378.62732.85124.00560.03950.19760.2916-0.35190.10810.3805-0.1106-0.1354-0.14770.0620.0049-0.02940.03630.0170.0447-25.51870.44754.6442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 177
2X-RAY DIFFRACTION2B17 - 24

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