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- PDB-2dh3: Crystal Structure of human ED-4F2hc -

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Basic information

Entry
Database: PDB / ID: 2dh3
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 / ZN interaction / coordination / dimerization / 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) / 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 / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / exogenous protein binding / anchoring junction / amino acid transport / Basigin interactions / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / calcium ion transport / double-stranded RNA binding / melanosome / virus receptor activity / basolateral plasma membrane / carbohydrate metabolic process / symbiont entry into host cell / cadherin binding / 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
Amino acid transporter heavy chain SLC3A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,5843
Polymers93,5192
Non-polymers651
Water50428
1
A: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8252
Polymers46,7591
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4F2 cell-surface antigen heavy chain


Theoretical massNumber of molelcules
Total (without water)46,7591
Polymers46,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.497, 101.786, 121.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 46759.496 Da / Num. of mol.: 2 / 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG 3350, 0,2M AMMONIUM SULFATE, pH 6, 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: 2.8→29.65 Å / Num. all: 19650 / Num. obs: 19650 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.0665 / Net I/σ(I): 15.74
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.46 / Rsym value: 0.3885 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→25 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.893 / SU B: 38.166 / SU ML: 0.346 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27508 1066 5.1 %RANDOM
Rwork0.21677 ---
all0.21972 19304 --
obs0.21972 19304 94.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.063 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å20 Å2
2---1.65 Å20 Å2
3---3.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6504 0 1 28 6533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226649
X-RAY DIFFRACTIONr_bond_other_d0.0010.025998
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9729020
X-RAY DIFFRACTIONr_angle_other_deg0.732313988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6015835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9724.582299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.795151119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.891536
X-RAY DIFFRACTIONr_chiral_restr0.0550.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027450
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021324
X-RAY DIFFRACTIONr_nbd_refined0.1780.21157
X-RAY DIFFRACTIONr_nbd_other0.1590.25589
X-RAY DIFFRACTIONr_nbtor_refined0.1660.23119
X-RAY DIFFRACTIONr_nbtor_other0.0770.23883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1390.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3061.55361
X-RAY DIFFRACTIONr_mcbond_other0.0271.51708
X-RAY DIFFRACTIONr_mcangle_it0.33826634
X-RAY DIFFRACTIONr_scbond_it0.35332923
X-RAY DIFFRACTIONr_scangle_it0.5714.52386
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 83 -
Rwork0.265 1436 -
obs--96.44 %
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)
12.3771-0.72630.35312.0151-0.06781.3279-0.0108-0.1918-0.03250.22930.00830.0213-0.0845-0.00560.0025-0.1352-0.03160.0216-0.1301-0.025-0.23622.550663.773848.0242
22.1815-0.4118-0.34762.38060.15751.1911-0.0138-0.13410.0960.29220.0333-0.07580.0348-0.0111-0.0195-0.1108-0.0261-0.0076-0.1010.0012-0.191912.275216.345241.007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA114 - 5299 - 424
2X-RAY DIFFRACTION1AC6011
3X-RAY DIFFRACTION2BB109 - 5294 - 424

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