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- PDB-6s8v: Structure of the high affinity Anticalin P3D11 in complex with th... -

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Basic information

Entry
Database: PDB / ID: 6s8v
TitleStructure of the high affinity Anticalin P3D11 in complex with the human CD98 heavy chain ectodomain
Components
  • 4F2 cell-surface antigen heavy chain
  • Neutrophil gelatinase-associated lipocalin
KeywordsPROTEIN BINDING / Lipocalin / Lcn2 / Anticalin / lipocalin-based binding protein / CD98hc / 4F2hc / amino acid transport / presentation of CD98 light chains / interaction with integrin beta subunits / single-pass type II membrane protein
Function / homology
Function and homology information


neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / methionine transport / tyrosine transport / L-histidine transport / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / : / L-leucine import across plasma membrane ...neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / methionine transport / tyrosine transport / L-histidine transport / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / isoleucine transport / L-alanine import across plasma membrane / phenylalanine transport / valine transport / L-leucine transmembrane transporter activity / calcium:sodium antiporter activity / L-leucine transport / thyroid hormone transport / proline transport / siderophore transport / Metal sequestration by antimicrobial proteins / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / exogenous protein binding / iron ion sequestering activity / enterobactin binding / anchoring junction / amino acid transport / Basigin interactions / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / Iron uptake and transport / specific granule lumen / calcium ion transport / double-stranded RNA binding / melanosome / virus receptor activity / positive regulation of cold-induced thermogenesis / basolateral plasma membrane / Interleukin-4 and Interleukin-13 signaling / carbohydrate metabolic process / defense response to bacterium / symbiont entry into host cell / cadherin binding / iron ion binding / apical plasma membrane / protein heterodimerization activity / lysosomal membrane / innate immune response / apoptotic process / synapse / Neutrophil degranulation / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / plasma membrane
Similarity search - Function
Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Calycin beta-barrel core domain ...Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Glycosyl hydrolase, all-beta / Calycin / Lipocalin / Lipocalin signature. / Glycoside hydrolase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Amino acid transporter heavy chain SLC3A2 / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchiefner, A. / Deuschle, F.-C. / Skerra, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCollaborative Research Centre 824 project A8 Germany
CitationJournal: Theranostics / Year: 2020
Title: Development of a high affinity Anticalin®directed against human CD98hc for theranostic applications.
Authors: Deuschle, F.C. / Morath, V. / Schiefner, A. / Brandt, C. / Ballke, S. / Reder, S. / Steiger, K. / Schwaiger, M. / Weber, W. / Skerra, A.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
B: 4F2 cell-surface antigen heavy chain
C: Neutrophil gelatinase-associated lipocalin
D: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,4207
Polymers137,2344
Non-polymers1863
Water16,123895
1
A: Neutrophil gelatinase-associated lipocalin
B: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7414
Polymers68,6172
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-1 kcal/mol
Surface area25270 Å2
MethodPISA
2
C: Neutrophil gelatinase-associated lipocalin
D: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6793
Polymers68,6172
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-5 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.809, 46.052, 137.092
Angle α, β, γ (deg.)90.000, 106.640, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / Siderocalin / p25


Mass: 21131.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Plasmid: pNGAL118 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P80188
#2: Protein 4F2 cell-surface antigen heavy chain / / 4F2hc / 4F2 heavy chain antigen / Lymphocyte activation antigen 4F2 large subunit / Solute carrier ...4F2hc / 4F2 heavy chain antigen / Lymphocyte activation antigen 4F2 large subunit / Solute carrier family 3 member 2


Mass: 47485.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC3A2, MDU1 / Plasmid: pASK-IBA5(+) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P08195
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 895 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.75 / Details: 18 % (w/v) PEG3350, 100 mM sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 113253 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.781 % / Biso Wilson estimate: 37.366 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Χ2: 1.036 / Net I/σ(I): 23.86 / Num. measured all: 768006 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.97.0380.8652.3211854616863168440.8330.93499.9
1.9-26.9240.4154.789454013674136530.950.44999.8
2-2.56.5610.11914.5526269840091400400.9950.12999.9
2.5-37.1230.04834.0212697917853178260.9990.05299.8
3-3.56.8620.03448.0862637915891280.9990.03699.7
3.5-46.2950.02756.0432185511651130.9990.0399.9
4-66.4710.02362.9548040743474240.9990.02599.9
6-87.2320.02266.48134221859185610.02499.8
8-107.0710.0271.5466765766010.022100
10-306.0540.02364.34429276070910.02593.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DH2, 4GH7

2dh2

4gh7


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.836 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.125
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 2234 2 %RANDOM
Rwork0.1845 ---
obs0.1853 111018 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.39 Å2 / Biso mean: 34.081 Å2 / Biso min: 15.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å2-0 Å2-0.35 Å2
2--0.56 Å20 Å2
3----0.71 Å2
Refinement stepCycle: final / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9248 0 12 897 10157
Biso mean--32.04 39.27 -
Num. residues----1180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199603
X-RAY DIFFRACTIONr_bond_other_d0.0010.028784
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.96213037
X-RAY DIFFRACTIONr_angle_other_deg1.057320461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67651206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1524.508437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.253151611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0231550
X-RAY DIFFRACTIONr_chiral_restr0.1130.21416
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021971
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.67 187 -
Rwork0.608 8149 -
all-8336 -
obs--99.93 %
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)
12.7220.16221.16621.8640.2514.6410.02710.0148-0.0583-0.06120.00870.19690.1605-0.1393-0.03590.0210.00330.01860.01990.00450.1119-42.160413.080612.1832
25.77571.32452.0843.11391.18723.05740.14310.1715-0.299-0.0936-0.0316-0.12360.20660.126-0.11150.04570.00870.02980.0573-0.00320.078-34.08017.76226.5108
33.90351.2814-1.42378.49942.29162.0448-0.10950.2305-0.1042-0.00470.04070.103-0.07080.16750.06880.33150.0008-0.00640.24740.00680.3093-39.2028-10.81359.4067
43.0615-0.2702-0.43954.7903-0.80733.77880.0104-0.0668-0.3190.0939-0.07280.27070.3815-0.13460.06240.0489-0.0070.0050.0874-0.01750.102-46.14248.266710.5458
53.7298-0.29550.06212.3202-0.12122.46140.0017-0.10520.20850.11320.02610.0998-0.0979-0.0971-0.02790.02310.01210.03160.049-0.02050.0852-42.613418.9418.2745
62.0535-0.445-0.2211.80170.84722.65910.0485-0.16140.06180.018-0.02480.14620.0037-0.2239-0.02370.0245-0.01180.04230.11880.02910.1063-34.76642.829244.6086
74.97230.6552-1.40620.6398-0.35541.4360.0547-0.36170.13570.1921-0.0423-0.145-0.00710.1971-0.01240.09370.0039-0.01190.178-0.01730.1195-21.18364.520951.7859
86.2752.2885-1.88413.36910.16727.131-0.03760.36440.0644-0.45470.0256-0.136700.25550.01190.09450.06850.01480.18690.00040.1357-5.4003-1.839641.0962
92.3597-0.88781.48091.0864-0.47862.8660.16760.1198-0.1729-0.0231-0.0368-0.11870.37440.4076-0.13070.06250.04770.00730.1223-0.0270.1306-17.4506-7.279430.4196
102.76240.92970.65563.7064-3.52746.43090.17530.3236-0.7508-0.0184-0.2253-0.57281.09181.01360.050.51850.3034-0.05780.4058-0.14880.3764-6.2908-21.12527.8494
113.00840.6839-0.79982.1241-0.65682.54750.02330.1502-0.11340.0893-0.046-0.08940.1880.18740.02280.04870.02330.02850.1938-0.01020.05613.1827-5.09961.7242
122.17430.00820.35516.5016-1.96184.01060.03120.1767-0.0905-0.33210.01060.13540.5332-0.1753-0.04170.09290.00560.03270.1938-0.01460.10843.7621-7.221155.1049
131.5319-1.5468-0.75921.58770.41779.701-0.0625-0.13210.04740.07270.0787-0.01260.12340.0846-0.01620.3490.01560.00820.3351-0.01510.346511.1671-25.565749.6046
142.8182-0.6051-0.60382.69320.72253.73880.05950.1758-0.25620.02790.08-0.30760.70690.3433-0.13960.16220.0722-0.0090.2061-0.00120.137213.8581-12.293760.4555
153.8615-0.86420.48663.0005-0.24112.92220.0462-0.0180.28090.1786-0.0557-0.1501-0.10670.21910.00950.053-0.00950.04610.20810.02440.088917.66351.03463.5022
161.84370.84560.4141.62110.98722.394-0.0009-0.0792-0.0220.10020.041-0.1543-0.00080.1555-0.04010.02330.01350.02190.19510.00960.121937.69377.885135.3521
176.5162-0.64410.3120.0754-0.040.0353-0.1937-0.31650.43790.05780.0976-0.0286-0.0412-0.09080.09610.51430.0322-0.02520.5314-0.07140.615311.721916.648524.1602
182.3249-0.25110.12424.75250.34894.6283-0.01040.30250.3005-0.4591-0.07060.5004-0.5291-0.38940.08090.10190.059-0.03920.22170.02990.196823.812614.624121.1355
191.14270.1425-0.64060.9051-0.49384.0498-0.01390.157-0.007-0.11230.10660.2185-0.0241-0.3266-0.09270.0242-0.01280.00080.22560.03040.153717.66720.680124.4844
203.1559-0.7848-1.80522.12961.50627.71430.06060.2905-0.4404-0.2606-0.06220.52850.4908-0.66520.00160.1178-0.0423-0.07390.3780.00330.373110.3474-3.440310.2895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 61
2X-RAY DIFFRACTION2A62 - 97
3X-RAY DIFFRACTION3A98 - 103
4X-RAY DIFFRACTION4A104 - 130
5X-RAY DIFFRACTION5A131 - 178
6X-RAY DIFFRACTION6B114 - 234
7X-RAY DIFFRACTION7B235 - 305
8X-RAY DIFFRACTION8B306 - 330
9X-RAY DIFFRACTION9B331 - 484
10X-RAY DIFFRACTION10B485 - 529
11X-RAY DIFFRACTION11C8 - 59
12X-RAY DIFFRACTION12C60 - 95
13X-RAY DIFFRACTION13C96 - 102
14X-RAY DIFFRACTION14C103 - 130
15X-RAY DIFFRACTION15C131 - 179
16X-RAY DIFFRACTION16D109 - 304
17X-RAY DIFFRACTION17D305 - 313
18X-RAY DIFFRACTION18D314 - 338
19X-RAY DIFFRACTION19D339 - 488
20X-RAY DIFFRACTION20D489 - 528

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