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- PDB-7lf7: Fab 6D12 bound to ApoL1 NTD -

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Basic information

Entry
Database: PDB / ID: 7lf7
TitleFab 6D12 bound to ApoL1 NTD
Components
  • (Fab 6D12 heavy ...) x 2
  • Apolipoprotein L1
  • Fab 6D12 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 / Apolipoprotein L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.026 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab 6D12 heavy chain
B: Fab 6D12 light chain
H: Fab 6D12 heavy chain
K: Apolipoprotein L1
L: Fab 6D12 light chain
M: Apolipoprotein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,71612
Polymers126,2556
Non-polymers4616
Water6,215345
1
A: Fab 6D12 heavy chain
B: Fab 6D12 light chain
M: Apolipoprotein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3506
Polymers63,1203
Non-polymers2303
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Fab 6D12 heavy chain
K: Apolipoprotein L1
L: Fab 6D12 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3666
Polymers63,1363
Non-polymers2303
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.103, 131.103, 87.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain H
12chain B
22chain L
13chain K
23chain M

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
11GLUGLULYSLYSchain AAA1 - 2221 - 222
21GLUGLUSERSERchain HHC1 - 2231 - 223
12ASPASPGLUGLUchain BBB1 - 2131 - 213
22ASPASPEOHEOHchain LLE - J1 - 3011
13SERSERLEULEUchain KKD65 - 14123 - 99
23SERSERLYSLYSchain MMF65 - 14223 - 100

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules KM

#4: 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: unidentified baculovirus / References: UniProt: O14791

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Antibody , 3 types, 4 molecules ABLH

#1: Antibody Fab 6D12 heavy chain


Mass: 24262.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab 6D12 light chain


Mass: 23568.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab 6D12 heavy chain


Mass: 24278.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 351 molecules

#5: Chemical ChemComp-EOH / ETHANOL


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.97 Å3/Da / Density % sol: 58.54 % / Description: Rods
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG 3350, 0.1M Ammonium Sulfate, 0.1M MES pH 6, 14mM sodium cholate
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 3, 2016 / Details: Si (111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.026→92.704 Å / Num. obs: 76896 / % possible obs: 95.1 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.051 / Rrim(I) all: 0.083 / Net I/σ(I): 12.8
Reflection shellResolution: 2.027→2.152 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3846 / CC1/2: 0.479 / Rpim(I) all: 0.797 / Rrim(I) all: 1.25 / % possible all: 64.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fvd

1fvd


Resolution: 2.026→41.458 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 3884 5.05 %
Rwork0.1886 73003 -
obs0.19 76887 80.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 250.77 Å2 / Biso mean: 69.0276 Å2 / Biso min: 29.05 Å2
Refinement stepCycle: final / Resolution: 2.026→41.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7953 0 74 345 8372
Biso mean--89.95 49.61 -
Num. residues----1024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038216
X-RAY DIFFRACTIONf_angle_d0.77111122
X-RAY DIFFRACTIONf_chiral_restr0.0291240
X-RAY DIFFRACTIONf_plane_restr0.0021415
X-RAY DIFFRACTIONf_dihedral_angle_d14.2262981
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2478X-RAY DIFFRACTION5.328TORSIONAL
12H2478X-RAY DIFFRACTION5.328TORSIONAL
21B2516X-RAY DIFFRACTION5.328TORSIONAL
22L2516X-RAY DIFFRACTION5.328TORSIONAL
31K984X-RAY DIFFRACTION5.328TORSIONAL
32M984X-RAY DIFFRACTION5.328TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0262-2.05090.4379150.32092618
2.0509-2.07690.3425200.324141313
2.0769-2.10420.38410.305573523
2.1042-2.13310.3044680.2983127539
2.1331-2.16350.3234890.2921162051
2.1635-2.19580.3231970.2806186758
2.1958-2.23010.34981090.2808206563
2.2301-2.26670.2561220.2707216668
2.2667-2.30580.28721500.2578239574
2.3058-2.34770.26891340.255255179
2.3477-2.39280.25341640.2448268984
2.3928-2.44170.24911720.24302393
2.4417-2.49480.27361790.23923214100
2.4948-2.55280.26791650.23243263100
2.5528-2.61660.30221620.23963276100
2.6166-2.68740.231570.22613246100
2.6874-2.76640.25341840.22133265100
2.7664-2.85570.2741490.22183226100
2.8557-2.95770.24011660.21083254100
2.9577-3.07610.22751670.2143267100
3.0761-3.21610.24961690.20123270100
3.2161-3.38560.21461610.20043222100
3.3856-3.59760.2051870.1864324499
3.5976-3.87510.19171660.1757325399
3.8751-4.26480.19941660.1523323999
4.2648-4.8810.16221590.1305324398
4.881-6.14640.16811800.1529321098
6.1464-41.4580.2031860.167325197
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)
11.9384-0.2129-0.30798.0251-0.47412.0755-0.34510.07190.00420.33540.57720.0098-0.08380.0914-0.1410.2756-0.0459-0.00760.4599-0.05190.4905-7.2552.994817.0751
26.3791-0.65920.17914.9303-2.06944.6229-0.1432-0.0505-0.3738-0.01240.077-0.40540.2570.25910.08980.3489-0.03080.0850.3643-0.06160.4165-7.583942.75414.3687
37.1057-0.4468-1.85366.2131.7935.7343-0.31060.4589-0.1876-0.31160.2052-0.12620.07920.4393-0.03340.3329-0.15040.07740.3444-0.03580.3611-10.945844.45645.6521
41.25110.67080.45892.59550.30691.5214-0.17050.3271-0.1547-0.21180.2304-0.13630.06820.2364-0.02950.3103-0.090.06580.3905-0.03390.4178-9.195546.614510.1171
54.2954-0.4142-3.63143.17311.06775.14180.0513-0.0480.13650.5507-0.16150.0808-0.3672-0.24450.12820.4659-0.0107-0.03280.34380.00220.4818-23.243572.223829.2237
65.1493-0.0999-2.9653.56280.50515.0645-0.0136-0.0937-0.05980.8802-0.18670.2715-0.2665-0.49190.24860.52060.010.00050.34450.01290.4567-25.669769.347531.897
73.1738-4.03240.71757.3449-1.66910.51380.1971-0.78880.42260.458-0.04030.30450.0219-0.23740.12550.7795-0.0703-0.02970.5452-0.18460.6257-21.212376.487936.5852
82.48560.6177-0.24852.14860.06121.9966-0.0050.03130.33850.00180.05410.06380.0783-0.0943-0.08830.3278-0.1120.0510.313-0.020.3865-29.122439.296811.7711
90.5240.1285-0.64195.0064-0.49282.19480.18140.13240.15610.7972-0.1620.6657-0.171-0.36650.0020.3930.05180.14210.414-0.04190.7212-35.143769.53925.7951
104.5986.1234-0.72859.3419-1.59172.8947-0.06160.50920.1875-0.1658-0.12030.22520.0288-0.31260.18860.44730.14160.06250.5204-0.04560.6701-38.222670.002720.7878
112.45711.4182-0.49555.4092-0.75982.01850.16310.26070.64020.0076-0.12641.1208-0.3144-0.5128-0.07460.45170.12640.05410.52230.01710.8221-37.781974.845320.9652
124.4205-1.0372-0.30796.6382-0.94273.32220.088-0.0171-0.2431-1.02550.09270.05340.759-0.1660.0350.29970.00250.00180.3123-0.01770.32161.569677.4433-12.6749
134.7581-0.2285-0.11884.3031-0.82532.7997-0.03280.0130.5778-0.0759-0.0352-0.0635-0.3804-0.01420.03250.31160.0444-0.01370.34-0.01770.3895-0.518787.4913-9.6587
145.57440.02010.39835.12770.60933.89880.0124-0.33060.13180.21880.11810.1979-0.05590.06120.07290.31720.1058-0.0460.388-0.03420.3492-3.397284.9245-0.9866
154.19590.4858-0.52395.0253-1.37683.2472-0.0621-0.69990.21420.4802-0.18160.0140.0440.5960.08660.27580.0849-0.06230.4239-0.11550.32754.001983.5581-1.5391
164.8729-0.61850.72294.74340.47882.34980.0369-0.5195-0.56720.5853-0.1262-0.383-0.0746-0.03030.11850.35240.060.02510.4838-0.00190.35732.90776.5966-4.7072
170.96460.88220.46513.81181.26110.84020.0406-0.15010.1407-0.0263-0.0923-0.2614-0.0852-0.1974-0.0360.25620.08430.00670.310.03310.3259-5.552378.1543-11.3899
186.2935-1.01912.63724.17641.1085.0460.3650.46370.2741-0.4386-0.3726-0.08710.2439-0.12840.09740.35470.03150.08060.2870.04940.313-15.196358.7612-27.4549
195.0431-1.47160.3353.4744-0.00031.9247-0.42931.6330.8057-0.8362-0.064-0.0726-0.86070.48870.00580.44240.04650.08310.43250.13430.3552-9.010859.2196-34.0057
207.24835.46545.14924.85554.59894.2880.06550.8156-0.6883-0.32080.0555-0.38920.27020.3807-0.15140.47280.08440.04520.4782-0.01890.5259-8.501653.0396-33.8722
213.4123-0.76920.32314.9379-0.15583.8342-0.024-1.1631.01090.50350.4541-0.9753-0.75230.8385-0.39490.81640.1212-0.00831.1791-0.51731.6128-6.948106.786819.3791
22-0.21210.17310.88388.64855.86712.895-0.0368-0.56521.29520.44370.1479-0.194-0.29820.3894-0.25150.8017-0.08210.12090.8432-0.51491.4988-10.6617115.931717.1418
234.04860.0891-0.1232.30730.27962.910.0505-0.095-0.21730.0820.06670.17610.1076-0.0886-0.09220.29430.1196-0.01150.3122-0.00650.3606-23.230188.0799-6.688
244.5070.03872.7351.84760.35183.92770.17390.2561-0.4438-0.39770.06540.0469-0.2689-0.1208-0.33440.41940.1143-0.04870.3927-0.01880.4602-23.932884.9276-13.822
252.14491.16890.76811.47171.8092.4399-0.1415-0.16920.0621-0.1085-0.26450.5482-0.0411-0.3989-0.00890.32140.103-0.05540.4075-0.02420.4612-22.995279.1454-9.3074
262.14880.31760.72695.2387-0.55475.70080.20370.6221-1.3656-0.2113-0.17620.06280.86290.0038-0.1330.5689-0.0586-0.0430.3243-0.03310.4674-15.995647.1022-25.3971
273.6407-3.00151.50035.65850.01754.1410.1848-0.549-0.35910.7211-0.0470.64920.2651-0.7616-0.09620.4056-0.20750.03080.47380.01350.3451-25.119854.0484-16.3371
283.9276-3.40780.6098.40520.19022.20060.20480.001-0.50960.3042-0.22680.48830.4355-0.4486-0.03780.4161-0.16850.01330.4282-0.02780.3766-25.425451.9536-20.4744
292.03562.00512.03012.04111.98872.02530.7085-0.52471.0462-1.25980.0784-5.1935-1.6272-0.0764-0.84820.7762-0.2096-0.45910.6982-0.17371.1104-22.740940.2497-33.4021
304.1423-1.7258-0.80282.53321.14143.01080.23831.4127-1.4727-1.9060.0166-1.41580.38270.2586-0.40861.3872-0.15570.51030.5909-0.29331.6495-11.150620.8613-13.4468
310.4666-1.163-0.20033.83032.9711.46890.20080.1425-1.1956-0.37540.4146-0.97660.20360.3934-0.54860.9788-0.07810.18450.5475-0.32581.6447-12.839211.4088-11.3745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )A1 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 40 )A18 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 60 )A41 - 60
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 119 )A61 - 119
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 165 )A120 - 165
6X-RAY DIFFRACTION6chain 'A' and (resid 166 through 211 )A166 - 211
7X-RAY DIFFRACTION7chain 'A' and (resid 212 through 222 )A212 - 222
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 102 )B1 - 102
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 128 )B103 - 128
10X-RAY DIFFRACTION10chain 'B' and (resid 129 through 150 )B129 - 150
11X-RAY DIFFRACTION11chain 'B' and (resid 151 through 213 )B151 - 213
12X-RAY DIFFRACTION12chain 'H' and (resid 1 through 17 )H1 - 17
13X-RAY DIFFRACTION13chain 'H' and (resid 18 through 40 )H18 - 40
14X-RAY DIFFRACTION14chain 'H' and (resid 41 through 60 )H41 - 60
15X-RAY DIFFRACTION15chain 'H' and (resid 61 through 76 )H61 - 76
16X-RAY DIFFRACTION16chain 'H' and (resid 77 through 91 )H77 - 91
17X-RAY DIFFRACTION17chain 'H' and (resid 92 through 132 )H92 - 132
18X-RAY DIFFRACTION18chain 'H' and (resid 133 through 196 )H133 - 196
19X-RAY DIFFRACTION19chain 'H' and (resid 197 through 211 )H197 - 211
20X-RAY DIFFRACTION20chain 'H' and (resid 212 through 223 )H212 - 223
21X-RAY DIFFRACTION21chain 'K' and (resid 65 through 90 )K65 - 90
22X-RAY DIFFRACTION22chain 'K' and (resid 91 through 141 )K91 - 141
23X-RAY DIFFRACTION23chain 'L' and (resid 1 through 75 )L1 - 75
24X-RAY DIFFRACTION24chain 'L' and (resid 76 through 90 )L76 - 90
25X-RAY DIFFRACTION25chain 'L' and (resid 91 through 113 )L91 - 113
26X-RAY DIFFRACTION26chain 'L' and (resid 114 through 128 )L114 - 128
27X-RAY DIFFRACTION27chain 'L' and (resid 129 through 163 )L129 - 163
28X-RAY DIFFRACTION28chain 'L' and (resid 164 through 213 )L164 - 213
29X-RAY DIFFRACTION29chain 'L' and (resid 214 through 214 )L214
30X-RAY DIFFRACTION30chain 'M' and (resid 65 through 90 )M65 - 90
31X-RAY DIFFRACTION31chain 'M' and (resid 91 through 142 )M91 - 142

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