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- PDB-7lfd: Fab 7D6 bound to ApoL1 BH3 like peptide -

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Basic information

Entry
Database: PDB / ID: 7lfd
TitleFab 7D6 bound to ApoL1 BH3 like peptide
Components
  • Apolipoprotein L1 BH3 like peptide
  • Fab 7D6 heavy chain
  • Fab 7D6 light chain
KeywordsIMMUNE SYSTEM / Complex
Function / homology
Function and homology information


lipoprotein metabolic process / high-density lipoprotein particle / very-low-density lipoprotein particle / cytolysis by host of symbiont cells / lipid transport / chloride channel activity / Scavenging of heme from plasma / cholesterol metabolic process / chloride transmembrane transport / Post-translational protein phosphorylation ...lipoprotein metabolic process / high-density lipoprotein particle / very-low-density lipoprotein particle / cytolysis by host of symbiont cells / lipid transport / chloride channel activity / Scavenging of heme from plasma / cholesterol metabolic process / chloride transmembrane transport / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood microparticle / endoplasmic reticulum lumen / innate immune response / lipid binding / extracellular space / extracellular region / membrane
Similarity search - Function
Apolipoprotein L / Apolipoprotein L / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ETHANOL / CITRATE ANION / AMMONIUM ION / Apolipoprotein L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.157 Å
AuthorsUltsch, M. / Kirchhofer, D.
CitationJournal: Commun Biol / Year: 2021
Title: Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif.
Authors: Ultsch, M. / Holliday, M.J. / Gerhardy, S. / Moran, P. / Scales, S.J. / Gupta, N. / Oltrabella, F. / Chiu, C. / Fairbrother, W. / Eigenbrot, C. / Kirchhofer, D.
History
DepositionJan 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein L1 BH3 like peptide
H: Fab 7D6 heavy chain
L: Fab 7D6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8639
Polymers49,3343
Non-polymers5296
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-30 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.947, 129.947, 90.817
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide Apolipoprotein L1 BH3 like peptide / Apolipoprotein L / ApoL / Apolipoprotein L-I / ApoL-I


Mass: 1957.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14791

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fab 7D6 heavy chain


Mass: 24050.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: AEP1 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4
#3: Antibody Fab 7D6 light chain


Mass: 23325.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: AEP1 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4

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Non-polymers , 5 types, 191 molecules

#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDescription: rods
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8M Ammonium Citrate pH 7.0 / PH range: 6.5 - 7.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.157→70.674 Å / Num. obs: 40614 / % possible obs: 89.6 % / Redundancy: 9.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.074 / Rrim(I) all: 0.167 / Net I/σ(I): 11.3
Reflection shellResolution: 2.163→2.273 Å / Rmerge(I) obs: 1.638 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2033 / CC1/2: 0.371 / Rpim(I) all: 0.855 / Rrim(I) all: 1.855

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LFB

7lfb


Resolution: 2.157→70.674 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2028 2262 5.57 %
Rwork0.1655 38325 -
obs0.1676 40587 84.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.8 Å2 / Biso mean: 46.5584 Å2 / Biso min: 22.1 Å2
Refinement stepCycle: final / Resolution: 2.157→70.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 74 185 3715
Biso mean--75.47 49.57 -
Num. residues----455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063575
X-RAY DIFFRACTIONf_angle_d0.9584844
X-RAY DIFFRACTIONf_chiral_restr0.035544
X-RAY DIFFRACTIONf_plane_restr0.004621
X-RAY DIFFRACTIONf_dihedral_angle_d13.8741290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1574-2.20430.35310.274155720
2.2043-2.25560.3178500.262981830
2.2556-2.3120.31971110.2761191468
2.312-2.37450.26461460.2463244988
2.3745-2.44440.30091560.2472268996
2.4444-2.52330.29191660.2364275799
2.5233-2.61350.26621630.24322800100
2.6135-2.71810.31251390.2406238384
2.7181-2.84190.25851610.19732817100
2.8419-2.99170.22041680.18292825100
2.9917-3.17910.23251670.18132807100
3.1791-3.42460.23571640.1715275798
3.4246-3.76920.19221420.1467229687
3.7692-4.31450.15281530.1216261391
4.3145-5.43560.1291690.10932862100
5.4356-70.6740.17081760.14712981100
Refinement TLS params.Method: refined / Origin x: 115.9727 Å / Origin y: 82.7508 Å / Origin z: 6.8589 Å
111213212223313233
T0.2951 Å20.0241 Å20.0025 Å2-0.2087 Å20.0296 Å2--0.2589 Å2
L1.722 °20.8697 °20.1749 °2-0.9065 °20.4616 °2--1.2367 °2
S-0.065 Å °0.0709 Å °-0.0199 Å °-0.0377 Å °0.0319 Å °0.0739 Å °-0.0649 Å °-0.0533 Å °0.0331 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA152 - 168
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1 - 3
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allH1 - 224
6X-RAY DIFFRACTION1allH301
7X-RAY DIFFRACTION1allL1 - 214
8X-RAY DIFFRACTION1allS1 - 206

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