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- PDB-6sua: Structure of the high affinity engineered lipocalin C1B12 in comp... -

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Basic information

Entry
Database: PDB / ID: 6sua
TitleStructure of the high affinity engineered lipocalin C1B12 in complex with the mouse 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 chain / interaction with integrin beta subunit / single-pass type II membrane protein
Function / homology
Function and homology information


Tryptophan catabolism / Amino acid transport across the plasma membrane / Basigin interactions / positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / apical pole of neuron / tyrosine transport / L-histidine transport ...Tryptophan catabolism / Amino acid transport across the plasma membrane / Basigin interactions / positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / aromatic amino acid transmembrane transporter activity / phenylalanine transport / methionine transport / positive regulation of cell projection organization / L-leucine transmembrane transporter activity / isoleucine transport / valine transport / proline transport / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / L-leucine transport / thyroid hormone transport / response to mycotoxin / cellular response to increased oxygen levels / response to blue light / response to fructose / cellular response to X-ray / short-term memory / exogenous protein binding / cellular response to interleukin-6 / enterobactin binding / iron ion sequestering activity / response to herbicide / anchoring junction / response to iron(II) ion / positive regulation of reactive oxygen species biosynthetic process / response to exogenous dsRNA / tryptophan transport / cellular response to interleukin-1 / long-term memory / cellular response to nutrient levels / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of endothelial cell migration / acute-phase response / Iron uptake and transport / cellular response to nerve growth factor stimulus / response to virus / specific granule lumen / cellular response to hydrogen peroxide / cellular response to amyloid-beta / melanosome / cellular response to tumor necrosis factor / double-stranded RNA binding / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / protease binding / Interleukin-4 and Interleukin-13 signaling / basolateral plasma membrane / cellular response to hypoxia / carbohydrate metabolic process / defense response to bacterium / apical plasma membrane / iron ion binding / response to xenobiotic stimulus / protein heterodimerization activity / symbiont entry into host cell / lysosomal membrane / innate immune response / neuronal cell body / synapse / Neutrophil degranulation / positive regulation of gene expression / cell surface / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane
Similarity search - Function
Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / Lipocalin / Lipocalin family conserved site / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II ...Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / Lipocalin / Lipocalin family conserved site / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Glycosyl hydrolase, all-beta / Calycin / Lipocalin / Glycosidases / Lipocalin signature. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Amino acid transporter heavy chain SLC3A2 / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSchiefner, A. / Deuschle, F.-C. / Skerra, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCollaborative Research Centre 824 project A8 Germany
CitationJournal: Protein Sci. / Year: 2020
Title: Design of a surrogate Anticalin protein directed against CD98hc for preclinical studies in mice.
Authors: Deuschle, F.C. / Schiefner, A. / Brandt, C. / Skerra, A.
History
DepositionSep 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.4Nov 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
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)140,81016
Polymers139,6584
Non-polymers1,15312
Water2,630146
1
A: Neutrophil gelatinase-associated lipocalin
B: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4058
Polymers69,8292
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-89 kcal/mol
Surface area25650 Å2
MethodPISA
2
C: Neutrophil gelatinase-associated lipocalin
D: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4058
Polymers69,8292
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-87 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.039, 107.737, 133.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLYAA5 - 1785 - 178
21SERSERGLYGLYCC5 - 1785 - 178
12VALVALALAALABB108 - 52616 - 434
22VALVALALAALADD108 - 52616 - 434

NCS ensembles :
ID
1
2

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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: 21462.252 Da / Num. of mol.: 2
Mutation: Q28H, A40G, I41N, Q49L, S68D, R72I, K73D, D77H, W79L, R81N, C87S, N96S, Y100T, P101L, L103S, Y106R, K125W, S127H, Y132W, K134Y
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 / Solute carrier family 3 member 2


Mass: 48366.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc3a2, Mdu1 / Plasmid: pASK-IBA5(+) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P10852
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12 %(w/v) PEG8000, 0.2 M Li2SO4

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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: Mar 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.75→34.71 Å / Num. obs: 39856 / % possible obs: 99.1 % / Redundancy: 13.198 % / Biso Wilson estimate: 42.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.197 / Rrim(I) all: 0.205 / Χ2: 0.944 / Net I/σ(I): 15.36 / Num. measured all: 526014 / Scaling rejects: 244
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
2.75-2.8511.7181.0792.4545630402938940.7691.12896.6
2.85-313.7180.8123.6869659508450780.9110.84399.9
3-3.213.990.5955.2775252538453790.9480.61899.9
3.2-3.513.7180.3469.1181496594759410.9780.3699.9
3.5-413.0230.214.9683320640463980.9920.20899.9
4-613.1890.09726.8120747926091550.9970.10198.9
6-812.2750.08827.7228183231022960.9980.09299.4
8-1013.0730.03749.631043284679810.03994.3
10-34.7112.3170.0362.171129594491710.03197.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I9Q, 6S8V

6i9q

6s8v


Resolution: 2.75→34.71 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.2251 / WRfactor Rwork: 0.1825 / FOM work R set: 0.7783 / SU B: 16.437 / SU ML: 0.314 / SU Rfree: 0.3831 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 1961 4.9 %RANDOM
Rwork0.2197 ---
obs0.2222 37895 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.8 Å2 / Biso mean: 43.758 Å2 / Biso min: 12.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0 Å2-0 Å2
2---3.22 Å20 Å2
3---4.07 Å2
Refinement stepCycle: final / Resolution: 2.75→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9424 0 60 146 9630
Biso mean--65.12 28.28 -
Num. residues----1186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0139698
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178894
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.63313168
X-RAY DIFFRACTIONr_angle_other_deg1.0681.57320694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29751182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39122.932498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.552151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8191552
X-RAY DIFFRACTIONr_chiral_restr0.0390.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022006
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A54040.06
12C54040.06
21B133080.05
22D133080.05
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 116 -
Rwork0.342 2701 -
all-2817 -
obs--97.07 %

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