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- PDB-7lf8: Fab 6D12 bound to ApoL2 NTD -

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Basic information

Entry
Database: PDB / ID: 7lf8
TitleFab 6D12 bound to ApoL2 NTD
Components
  • Apolipoprotein L2
  • Fab 6D12 heavy chain
  • Fab 6D12 light chain
KeywordsIMMUNE SYSTEM / Complex
Function / homology
Function and homology information


lipoprotein metabolic process / lipid transport / lipid binding / extracellular region / membrane
Similarity search - Function
Apolipoprotein L / Apolipoprotein L / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Apolipoprotein L2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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 L2
H: Fab 6D12 heavy chain
L: Fab 6D12 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5065
Polymers63,3193
Non-polymers1872
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-28 kcal/mol
Surface area23030 Å2
Unit cell
Length a, b, c (Å)97.903, 154.290, 88.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Apolipoprotein L2


Mass: 15408.214 Da / Num. of mol.: 1 / Fragment: residues 114-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOL2 / Production host: Baculoviridae sp. (virus) / References: UniProt: J3KQL8

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fab 6D12 heavy chain


Mass: 24342.133 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)
#3: Antibody Fab 6D12 light chain


Mass: 23568.330 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 , 3 types, 73 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.6 Å3/Da / Density % sol: 52.71 % / Description: Rods
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350, 0.2M Ammonium di-hydrogen phosphate, 14mM sodium cholate
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: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→82.665 Å / Num. obs: 25037 / % possible obs: 93.5 % / Redundancy: 8.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.286 / Rpim(I) all: 0.151 / Rrim(I) all: 0.325 / Net I/σ(I): 17.7
Reflection shellResolution: 2.16→2.394 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.776 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1254 / CC1/2: 0.106 / Rpim(I) all: 1.098 / Rrim(I) all: 2.102 / % possible all: 69

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LF7

7lf7


Resolution: 2.15→32.73 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.289 / SU Rfree Blow DPI: 0.215
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1206 4.82 %RANDOM
Rwork0.192 ---
obs0.194 25031 68.2 %-
Displacement parametersBiso max: 135.77 Å2 / Biso mean: 40.82 Å2 / Biso min: 13.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.0979 Å20 Å20 Å2
2---0.5278 Å20 Å2
3---1.6257 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.15→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 19 71 3839
Biso mean--82.1 33.38 -
Num. residues----486
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1600SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1164HARMONIC5
X-RAY DIFFRACTIONt_it7452HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion509SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7253SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7452HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13399HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion16.35
LS refinement shellResolution: 2.15→2.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3418 24 4.79 %
Rwork0.2348 477 -
all0.2404 501 -
obs--7.28 %
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)
10.28970.4739-0.53670.0938-0.19570.2832-0.00120.00790.0138-0.0027-0.0046-0.00010.00290.01260.00580.00990.00440.0381-0.0315-0.0048-0.014333.87038.598122.189
20.5791-0.4529-0.52320.91230.68340.30760.00570.00350.0069-0.00120.00860.0004-0.0072-0.0099-0.01430.02490.0135-0.0426-0.0661-0.0109-0.02524.47229.0349127.789
30-0.64330.42180.519-0.34220.3339-0.00290.00350.0442-0.01550.01280.010.00770.003-0.00980.02190.0655-0.0041-0.04410.00430.000325.884212.2115123.598
40-0.23850.01720-0.1380.0535-0.00080.00560.0076-0.001-0.00750.00090.00080.00710.00830.0055-0.0057-0.0148-0.0245-0.0177-0.025737.34121.5863108.467
500.003-0.22410-0.26520.44890.0127-0.00030.01990.00880.009-0.00460.00530.0047-0.0216-0.02040.0118-0.02790.01730.0509-0.02845.596118.89796.0231
60.13920.4593-0.34720.1125-0.07270.62410.01160.01220.01960.008-0.0392-0.00340.019-0.03380.0276-0.0505-0.00330.0370.02390.0559-0.021647.178116.479595.6198
70.2936-0.17440.40330.0188-0.85330.5027-0.0010.0006-0.0102-0.019-0.00540.0269-0.0092-0.03430.0064-0.02260.0319-0.0105-0.01590.03420.008712.753327.3351117.439
80-0.44320.03170.7081-0.50230.2496-0.00380.00240.01940.0104-0.00770.0292-0.0116-0.00860.01150.00140.05510.0305-0.04680.0345-0.03619.104927.5189125.543
900.021-0.37480.6796-1.23570.09030.001-0.0129-0.014-0.00830.0364-0.0092-0.0289-0.007-0.0374-0.00570.09190.0142-0.0350.03090.000516.637934.321120.663
100-0.9299-0.15330.029-0.346900.001-0.00070.0147-0.0041-0.00480.01620.013-0.02310.0038-0.00070.02320.012-0.01360.01730.018315.784921.0667123.51
110-0.92690.17650.1072-0.34130.7420.00110.02590.0080.0044-0.002-0.0046-0.01080.01280.00090.00110.0629-0.0005-0.0245-0.003-0.05133.402524.636891.8279
120-0.63960.57111.1068-0.27991.19740.01790.03560.0188-0.003-0.00510.0470.00210.0165-0.01280.01280.0445-0.03080.0172-0.0495-0.087929.830218.274789.4306
1300.2854-0.29950.25540.4130.07040.00060.0012-0.00630.0070.0026-0.0020.0038-0.0123-0.00310.0007-0.02170.0284-0.0409-0.0408-0.043317.788326.8846155.988
140-0.0067-0.08220-0.19190.0088-0.0001-0.0062-0.0009-0.0011-0.00250.00340.0026-0.00450.0026-0.00490.0178-0.001-0.015-0.0141-0.031814.323925.8199144.322
150-0.26990.112900.06910.10680.0016-0.0079-0.00150.0132-0.0011-0.00040.00070.0028-0.0006-0.0030.01160.0266-0.02120.009-0.022919.604618.8331152.333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{L|1 - 18}L1 - 18
2X-RAY DIFFRACTION2{L|19 - 75}L19 - 75
3X-RAY DIFFRACTION3{L|76 - 102}L76 - 102
4X-RAY DIFFRACTION4{L|103 - 113}L103 - 113
5X-RAY DIFFRACTION5{L|114 - 163}L114 - 163
6X-RAY DIFFRACTION6{L|164 - 212}L164 - 212
7X-RAY DIFFRACTION7{H|1 - 40}H1 - 40
8X-RAY DIFFRACTION8{H|41 - 60}H41 - 60
9X-RAY DIFFRACTION9{H|61 - 91}H61 - 91
10X-RAY DIFFRACTION10{H|92 - 117}H92 - 117
11X-RAY DIFFRACTION11{H|118 - 153}H118 - 153
12X-RAY DIFFRACTION12{H|154 - 222}H154 - 222
13X-RAY DIFFRACTION13{A|6 - 31}A6 - 31
14X-RAY DIFFRACTION14{A|32 - 45}A32 - 45
15X-RAY DIFFRACTION15{A|46 - 62}A46 - 62

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