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- PDB-2dh2: Crystal Structure of human ED-4F2hc -

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Basic information

Entry
Database: PDB / ID: 2dh2
TitleCrystal Structure of human ED-4F2hc
Components4F2 cell-surface antigen heavy chain
KeywordsTRANSPORT PROTEIN / SIGNALING PROTEIN / TIM-barrel / glycosidase like / antiparallel beta-sheet / greek key / C-terminal domain / extracellular domain
Function / homology
Function and homology information


neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / tyrosine transport / L-histidine transport / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / methionine transport / : / L-leucine import across plasma membrane ...neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / tyrosine transport / L-histidine transport / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / methionine transport / : / 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 / proline transport / calcium:sodium antiporter activity / L-leucine transport / thyroid hormone transport / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / exogenous protein binding / amino acid transport / anchoring junction / Basigin interactions / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / calcium ion transport / melanosome / double-stranded RNA binding / virus receptor activity / basolateral plasma membrane / carbohydrate metabolic process / cadherin binding / symbiont entry into host cell / apical plasma membrane / protein heterodimerization activity / lysosomal membrane / synapse / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / nucleoplasm / membrane / 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 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily ...Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Amino acid transporter heavy chain SLC3A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFort, J. / Fita, I. / Palacin, M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane.
Authors: Fort, J. / de la Ballina, L.R. / Burghardt, H.E. / Ferrer-Costa, C. / Turnay, J. / Ferrer-Orta, C. / Uson, I. / Zorzano, A. / Fernandez-Recio, J. / Orozco, M. / Lizarbe, M.A. / Fita, I. / Palacin, M.
History
DepositionMar 21, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0062
Polymers46,9471
Non-polymers591
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.674, 67.846, 73.949
Angle α, β, γ (deg.)90.00, 98.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 4F2 cell-surface antigen heavy chain / / 4F2hc / Lymphocyte activation antigen 4F2 large subunit / 4F2 heavy chain antigen / CD98 antigen


Mass: 46947.070 Da / Num. of mol.: 1 / Fragment: ED4F2hc(Ectodomain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC3A2, MDU1 / Plasmid: pTrcHis (Invitrogen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P08195
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 4000, 0,2M SODIUM ACETATE, 0,1M TRIS BUFFER, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9789 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 28, 2003 / Details: KB-MIRROR
RadiationMonochromator: liq N2 cooled Si-111 double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.1→19.8 Å / Num. all: 26350 / Num. obs: 22652 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.084 / Net I/σ(I): 14
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.541 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CaspRphasing
MOLREPphasing
DMMultiphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UOK, 1JI2 with Caspr MODELLER NORMAL MODES

1uok

1ji2


Resolution: 2.1→17.83 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.328 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.257 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22969 1136 5.1 %RANDOM
Rwork0.17495 ---
obs0.17777 20986 97.27 %-
all-20986 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.584 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.26 Å2
2---0.28 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→17.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 4 139 3412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223345
X-RAY DIFFRACTIONr_bond_other_d0.0010.023018
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.9734537
X-RAY DIFFRACTIONr_angle_other_deg0.84937039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1924.6150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67315562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8651518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02664
X-RAY DIFFRACTIONr_nbd_refined0.2070.2656
X-RAY DIFFRACTIONr_nbd_other0.1950.22979
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21623
X-RAY DIFFRACTIONr_nbtor_other0.0870.21899
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.11.52523
X-RAY DIFFRACTIONr_mcbond_other0.1791.5859
X-RAY DIFFRACTIONr_mcangle_it1.34323339
X-RAY DIFFRACTIONr_scbond_it1.94831415
X-RAY DIFFRACTIONr_scangle_it2.9164.51198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 72 -
Rwork0.209 1533 -
obs--98.71 %
Refinement TLS params.Method: refined / Origin x: 6.955 Å / Origin y: 0.328 Å / Origin z: 18.924 Å
111213212223313233
T-0.1542 Å20.0001 Å2-0.0595 Å2--0.1118 Å20.0012 Å2---0.124 Å2
L1.1382 °2-0.1325 °2-0.6154 °2-1.3808 °20.2919 °2--2.1085 °2
S-0.001 Å °-0.0132 Å °-0.0226 Å °0.1999 Å °0.0065 Å °-0.1114 Å °0.1286 Å °0.1559 Å °-0.0055 Å °

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