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- PDB-7lfa: Fab 3B6 bound to ApoL1 NTD -

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Basic information

Entry
Database: PDB / ID: 7lfa
TitleFab 3B6 bound to ApoL1 NTD
Components
  • Apolipoprotein L1
  • Fab 3B6 heavy chain
  • Fab 3B6 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: 1.857 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 15, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 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
B: Fab 3B6 heavy chain
C: Apolipoprotein L1
D: Fab 3B6 light chain
H: Fab 3B6 heavy chain
L: Fab 3B6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,03910
Polymers123,7846
Non-polymers2554
Water6,954386
1
A: Apolipoprotein L1
B: Fab 3B6 heavy chain
D: Fab 3B6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0205
Polymers61,8923
Non-polymers1282
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-39 kcal/mol
Surface area24710 Å2
MethodPISA
2
C: Apolipoprotein L1
H: Fab 3B6 heavy chain
L: Fab 3B6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0205
Polymers61,8923
Non-polymers1282
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-32 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.753, 71.867, 123.436
Angle α, β, γ (deg.)80.160, 85.050, 90.160
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain H
13chain D
23chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEARGARGchain AAA66 - 15924 - 117
21GLUGLUVALVALchain CCC69 - 16827 - 126
12GLNGLNLYSLYSchain BBB1 - 2201 - 220
22GLNGLNLYSLYSchain HHE1 - 2201 - 220
13GLNGLNTHRTHRchain DDD1 - 2121 - 212
23GLNGLNTHRTHRchain LLF1 - 2121 - 212

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AC

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


Mass: 15289.139 Da / Num. of mol.: 2 / 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, 4 molecules BHDL

#2: Antibody Fab 3B6 heavy chain


Mass: 23916.699 Da / Num. of mol.: 2
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 3B6 light chain


Mass: 22686.207 Da / Num. of mol.: 2
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 , 3 types, 390 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 3.72 Å3/Da / Density % sol: 66.93 % / Description: plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 40% MPD, 5% PEG 8000, 0.1M Na Cacodylate pH 6.5 / 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: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.857→70.99 Å / Num. obs: 82724 / % possible obs: 89.6 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.059 / Net I/σ(I): 3.6
Reflection shellResolution: 1.858→2.044 Å / Redundancy: 3 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4136 / CC1/2: 0.635 / Rpim(I) all: 0.496 / Rrim(I) all: 0.701 / % possible all: 52.2

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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: 2VL5

2vl5


Resolution: 1.857→70.799 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 4035 4.88 %
Rwork0.2047 78601 -
obs0.2065 82636 55.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 233.76 Å2 / Biso mean: 55.7817 Å2 / Biso min: 16.25 Å2
Refinement stepCycle: final / Resolution: 1.857→70.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7841 0 30 386 8257
Biso mean--37.65 35.82 -
Num. residues----1058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118058
X-RAY DIFFRACTIONf_angle_d1.3110988
X-RAY DIFFRACTIONf_chiral_restr0.0481252
X-RAY DIFFRACTIONf_plane_restr0.0071406
X-RAY DIFFRACTIONf_dihedral_angle_d13.6482775
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A826X-RAY DIFFRACTION6.295TORSIONAL
12C826X-RAY DIFFRACTION6.295TORSIONAL
21B2466X-RAY DIFFRACTION6.295TORSIONAL
22H2466X-RAY DIFFRACTION6.295TORSIONAL
31D2389X-RAY DIFFRACTION6.295TORSIONAL
32L2389X-RAY DIFFRACTION6.295TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8572-1.87910.242730.24121042
1.8791-1.9020.222570.23531894
1.902-1.92610.3644220.2582846
1.9261-1.95140.2589230.24524259
1.9514-1.97820.2698330.263763613
1.9782-2.00640.2203460.24283217
2.0064-2.03640.281630.2231112423
2.0364-2.06820.2892830.2205169534
2.0682-2.10210.2304960.2162194539
2.1021-2.13840.25171140.2347196040
2.1384-2.17720.2589990.2222215643
2.1772-2.21910.23751170.2217211143
2.2191-2.26440.3297960.2379220945
2.2644-2.31370.26691120.2434234647
2.3137-2.36750.27171180.2548238449
2.3675-2.42670.25661570.2482257453
2.4267-2.49230.26291320.2612289758
2.4923-2.56570.28571480.2685307163
2.5657-2.64850.27861800.2561336868
2.6485-2.74310.29722100.2596368876
2.7431-2.8530.28582060.2572427987
2.853-2.98280.2942660.2376470296
2.9828-3.14010.27352290.2385483198
3.1401-3.33680.25922470.2035478697
3.3368-3.59440.22232530.1958478097
3.5944-3.95610.23162410.1813479497
3.9561-4.52850.18282340.1531472696
4.5285-5.70510.19922440.1618481197
5.7051-70.7990.22932560.19489499
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)
12.0598-0.0829-0.12412.44641.80611.3351-0.06140.4706-0.46390.26520.2067-0.11621.050.2566-0.05991.60020.05010.45371.1037-0.25740.773114.6096-63.9924-15.9069
20.5522-1.0558-1.56282.96593.92425.80730.2020.1577-0.1687-0.7664-0.1699-0.23770.14090.3682-0.59691.3354-0.02380.23091.6268-0.52560.71813.0887-63.102-22.7639
30.2425-0.0451-0.07941.8995-1.4782.895-0.18160.1510.1251-0.7799-0.131-0.81690.52680.6380.35120.9561-0.00390.26351.1895-0.03170.478719.9658-42.874-19.9124
42.68490.6669-1.81962.591-0.4832.2925-0.11320.7293-0.6029-0.59560.05610.29980.3431-0.170.02840.26350.0313-0.10790.4325-0.06380.3722-3.5277-54.05147.9787
51.977-0.85021.23122.9421-0.98571.98830.0223-0.11450.17390.1592-0.10140.1675-0.0483-0.12910.06930.14070.03610.01340.08570.07760.4987-27.7189-44.048723.7012
65.6176-0.9921-4.77795.36282.13724.3856-0.2023-0.0504-0.69440.06150.46780.1531.1248-0.5031-0.03331.553-0.2376-0.13011.24970.32971.2182-16.5285-26.713270.7598
71.3964-0.2329-0.63072.1012-2.00063.0046-0.1769-0.7577-0.92451.0038-0.0190.32620.8467-0.1616-0.43731.4764-0.14680.03441.25630.49730.7118-13.8372-23.389575.4229
85.84275.2397-5.61035.0093-5.17865.45740.278-1.0108-0.60171.60380.24411.67880.3132-1.3666-0.41931.0659-0.14890.26941.4760.11720.8109-21.3415-10.122969.5869
92.5390.0510.23832.41470.64890.1943-0.07260.8661-0.0646-0.7189-0.046-0.8966-0.64680.67390.21450.92830.05340.22061.33340.21141.0824-23.8897-11.940394.1256
101.5253-0.74520.61092.0578-0.06530.85340.22320.67070.5014-0.497-0.09680.1216-0.2765-0.29140.06150.28740.18420.01110.50280.26620.47642.8595-33.79973.8524
111.499-0.2211-0.28181.14540.99891.35790.1805-0.11110.2311-0.0348-0.2270.12130.284-0.0198-0.65230.20990.0542-0.03520.13210.14110.56-21.1187-33.865727.2596
121.9941-0.34930.15572.69920.62032.46930.0394-0.28380.14790.3329-0.19390.03330.1053-0.06780.06980.12490.0343-0.05320.13450.06970.586-21.4057-31.775534.5641
131.7073-0.5824-0.80491.92220.61731.0762-0.0027-0.6925-0.79680.6378-0.0006-0.27640.37550.0837-0.15740.3089-0.0437-0.20520.49420.30330.68781.6862-18.131946.6643
140.96660.24760.42391.69810.4980.9530.01660.0116-0.1979-0.1548-0.1267-0.0738-0.08330.07320.00360.1403-0.0507-0.030.04040.07630.69925.8606-8.094731.0963
153.3382-0.35390.87952.9564-0.06691.65150.1764-0.98080.0990.6551-0.0474-0.1631-0.28520.1701-0.09740.3185-0.1389-0.02960.4959-0.0240.2347-4.7881.933250.9277
162.20270.8233-1.18650.3077-0.44270.63780.493-0.30510.56770.2173-0.22610.2197-0.2219-0.009-0.22490.3155-0.10870.12040.2291-0.16070.50327.128513.09138.3327
172.4119-0.0738-0.44792.62330.02732.39130.07990.25590.0048-0.1758-0.15330.13290.18960.0253-0.01840.14390.0339-0.05110.09790.010.432919.52161.521622.3488
182.1028-0.5040.143.2-0.34313.06960.17190.58490.1425-0.576-0.185-0.28410.22360.24730.01730.18050.07320.02190.20070.04840.514423.01753.744316.8065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 66 through 90 )A66 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 125 )A91 - 125
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 159 )A126 - 159
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 125 )B1 - 125
5X-RAY DIFFRACTION5chain 'B' and (resid 126 through 220 )B126 - 220
6X-RAY DIFFRACTION6chain 'C' and (resid 69 through 90 )C69 - 90
7X-RAY DIFFRACTION7chain 'C' and (resid 91 through 133 )C91 - 133
8X-RAY DIFFRACTION8chain 'C' and (resid 134 through 146 )C134 - 146
9X-RAY DIFFRACTION9chain 'C' and (resid 147 through 168 )C147 - 168
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 103 )D1 - 103
11X-RAY DIFFRACTION11chain 'D' and (resid 104 through 132 )D104 - 132
12X-RAY DIFFRACTION12chain 'D' and (resid 133 through 212 )D133 - 212
13X-RAY DIFFRACTION13chain 'H' and (resid 1 through 125 )H1 - 125
14X-RAY DIFFRACTION14chain 'H' and (resid 126 through 220 )H126 - 220
15X-RAY DIFFRACTION15chain 'L' and (resid 1 through 103 )L1 - 103
16X-RAY DIFFRACTION16chain 'L' and (resid 104 through 116 )L104 - 116
17X-RAY DIFFRACTION17chain 'L' and (resid 117 through 174 )L117 - 174
18X-RAY DIFFRACTION18chain 'L' and (resid 175 through 212 )L175 - 212

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