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- PDB-7lfb: Fab 7D6 bound to ApoL1 NTD -

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Basic information

Entry
Database: PDB / ID: 7lfb
TitleFab 7D6 bound to ApoL1 NTD
Components
  • Apolipoprotein L1
  • 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.913 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 1.3Nov 13, 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
H: Fab 7D6 heavy chain
L: Fab 7D6 light chain
X: Apolipoprotein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2378
Polymers62,6663
Non-polymers5725
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-50 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.238, 60.262, 124.216
Angle α, β, γ (deg.)90.000, 111.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-523-

HOH

21X-226-

HOH

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Components

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Protein , 1 types, 1 molecules X

#3: Protein Apolipoprotein L1 / Apolipoprotein L / ApoL / Apolipoprotein L-I / ApoL-I


Mass: 15289.139 Da / Num. of mol.: 1 / Fragment: residues 61-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOL1, APOL / Production host: Baculoviridae sp. (virus) / References: UniProt: O14791

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Antibody , 2 types, 2 molecules HL

#1: 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
#2: 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 , 4 types, 411 molecules

#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: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.92 % / Description: blocks
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15%(w/v) PEG 4000, 0.15M Ammonium sulfate, 0.1M MES pH 6
PH range: 6.0 - 7.0

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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 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→49.628 Å / Num. obs: 51638 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.047 / Rrim(I) all: 0.068 / Net I/σ(I): 11.4
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3305 / CC1/2: 0.81 / Rpim(I) all: 0.339 / Rrim(I) all: 0.584 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVD

1fvd


Resolution: 1.913→49.628 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 2504 5.06 %
Rwork0.1677 46952 -
obs0.1692 49456 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.35 Å2 / Biso mean: 43.0132 Å2 / Biso min: 14.33 Å2
Refinement stepCycle: final / Resolution: 1.913→49.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 42 406 4439
Biso mean--58.74 43.38 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064161
X-RAY DIFFRACTIONf_angle_d0.9615643
X-RAY DIFFRACTIONf_chiral_restr0.038621
X-RAY DIFFRACTIONf_plane_restr0.004725
X-RAY DIFFRACTIONf_dihedral_angle_d14.3161514
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.913-1.94970.32561460.27082624100
1.9497-1.98950.2681390.232612100
1.9895-2.03280.22291400.21072612100
2.0328-2.080.24331550.1952640100
2.08-2.13210.2471620.18822602100
2.1321-2.18970.23251510.18372593100
2.1897-2.25410.20081350.18662660100
2.2541-2.32690.23161470.18261599
2.3269-2.41010.23541230.17832641100
2.4101-2.50650.1941380.18012618100
2.5065-2.62060.23171180.1787264899
2.6206-2.75880.24171280.1795263299
2.7588-2.93160.20561450.1725261499
2.9316-3.15790.19761330.1765258598
3.1579-3.47560.21091480.1625253496
3.4756-3.97840.20311250.1556253395
3.9784-5.01160.12251330.1316252594
5.0116-49.6280.16581380.154266497
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)
10.90940.0750.12331.09380.02411.4427-0.00550.1689-0.0234-0.10790.001-0.3138-0.14910.4088-0.0030.1698-0.01380.01790.2496-0.04030.313611.9392-1.137945.0917
21.30110.2086-0.29451.1365-0.00811.1004-0.0090.1235-0.0007-0.0868-0.0032-0.0529-0.0134-0.0140.01490.15850.0061-0.01140.1521-0.02950.2202-5.49961.022248.2706
30.6933-0.0074-0.06511.02190.12880.6291-0.01670.37190.1274-0.2401-0.07950.1677-0.4111-0.19340.05510.76620.00410.15870.9003-0.00970.2357-3.84955.9480.8943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'H' and resid 1 through 224)H1 - 224
2X-RAY DIFFRACTION2(chain 'L' and resid 1 through 214)L1 - 214
3X-RAY DIFFRACTION3(chain 'X' and resid 91 through 170)X91 - 170

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