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- PDB-4kmy: Human folate receptor beta (FOLR2) at neutral pH -

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Basic information

Entry
Database: PDB / ID: 4kmy
TitleHuman folate receptor beta (FOLR2) at neutral pH
ComponentsFolate receptor beta
KeywordsMEMBRANE PROTEIN / Folate Receptor Beta / FOLR2 / GPI-anchor membrane receptor / Folic acid / folates / 5-methyltetrahydrofolate / antifolates / folate-conjugates / TRANSPORT PROTEIN
Function / homology
Function and homology information


folic acid receptor activity / folic acid transport / sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / Post-translational modification: synthesis of GPI-anchored proteins / Metabolism of folate and pterines / folic acid binding / signaling receptor activity / cell adhesion / inflammatory response ...folic acid receptor activity / folic acid transport / sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / Post-translational modification: synthesis of GPI-anchored proteins / Metabolism of folate and pterines / folic acid binding / signaling receptor activity / cell adhesion / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / cell surface / extracellular region / plasma membrane
Similarity search - Function
Folate receptor / Folate receptor-like / Folate receptor family
Similarity search - Domain/homology
: / Folate receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 Å
AuthorsWibowo, A.S. / Dann III, C.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of human folate receptors reveal biological trafficking states and diversity in folate and antifolate recognition.
Authors: Wibowo, A.S. / Singh, M. / Reeder, K.M. / Carter, J.J. / Kovach, A.R. / Meng, W. / Ratnam, M. / Zhang, F. / Dann, C.E.
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Folate receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2823
Polymers24,0221
Non-polymers2602
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.026, 75.026, 97.188
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Folate receptor beta / FR-beta / Folate receptor 2 / Folate receptor / fetal/placental / Placental folate-binding protein / FBP


Mass: 24021.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOLR2 / Plasmid: pSGHV0 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14207
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.0 M Ammonium citrate tribasic, pH 7.0, 0.1 M Bis-Tris Propane, pH 7.0, Vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 2, 2011
Details: The NOIR-1 detector was built by E. Westbrook; 180 cm lens focused CCD
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 28977 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.093 / Χ2: 0.875 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.79-1.833.70.45514700.68199.7
1.83-1.864.20.41514210.547199.9
1.86-1.94.50.39414190.6199.9
1.9-1.944.70.32614460.58199.9
1.94-1.984.70.27214600.718199.9
1.98-2.034.70.23714480.736199.9
2.03-2.084.80.21514340.791199.9
2.08-2.134.80.17614340.998199.9
2.13-2.24.80.1514561.018199.9
2.2-2.274.70.14514380.7821100
2.27-2.354.80.13114361.0161100
2.35-2.444.80.12514561.0781100
2.44-2.554.80.11514571.0381100
2.55-2.694.80.11214430.9071100
2.69-2.864.80.1114451.0131100
2.86-3.084.80.10914551.0021100
3.08-3.394.80.09714511.0421100
3.39-3.884.80.08514510.9611100
3.88-4.884.80.06914640.867199.8
4.88-504.70.07414930.97199.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KMZ

4kmz


Resolution: 1.795→37.513 Å / Occupancy max: 1 / Occupancy min: 0.6 / FOM work R set: 0.8952 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 17.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 1199 4.14 %
Rwork0.1638 --
obs0.1649 28939 99.84 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.735 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 85.91 Å2 / Biso mean: 32.0993 Å2 / Biso min: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.3435 Å2-0 Å2-0 Å2
2--0.3435 Å2-0 Å2
3----0.6871 Å2
Refinement stepCycle: LAST / Resolution: 1.795→37.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 15 164 1846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091745
X-RAY DIFFRACTIONf_angle_d1.1132357
X-RAY DIFFRACTIONf_chiral_restr0.084232
X-RAY DIFFRACTIONf_plane_restr0.006306
X-RAY DIFFRACTIONf_dihedral_angle_d11.821624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7953-1.86720.24891510.21233035318699
1.8672-1.95220.24811340.19130713205100
1.9522-2.05510.22471360.17530593195100
2.0551-2.18380.19711280.160630743202100
2.1838-2.35240.21121300.16631263256100
2.3524-2.58910.20341360.178630533189100
2.5891-2.96360.23051200.178130933213100
2.9636-3.73330.18451440.158930943238100
3.7333-37.52120.1561200.14731353255100
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)
12.78351.00170.21173.523-1.00424.31640.0397-0.2692-0.4885-0.0592-0.1503-0.330.64710.13630.11940.29990.05010.01650.26190.05110.31419.5282-47.59971.5277
22.56-0.47220.13425.61-0.49773.5335-0.0249-0.00590.09480.0262-0.0552-0.66450.21160.56570.07380.16050.02660.00960.27510.00860.288815.1516-39.1754-1.9076
32.3608-0.07351.07080.8250.02431.5748-0.02190.20850.0841-0.2469-0.0942-0.09120.03720.04690.10740.20690.01180.02990.2387-0.00040.21485.423-32.8741-10.8319
42.96650.5441-0.04073.07131.53354.29970.0880.0499-0.3047-0.1402-0.22070.19510.6314-0.4520.10790.3351-0.0520.00450.25350.02560.244-1.7025-46.13661.4386
52.73110.39820.10335.5022-3.1374.4938-0.004-0.50080.60.6866-0.1333-0.0929-0.5551-0.04220.14650.209-0.0065-0.03150.2679-0.08830.30261.8392-25.06464.1939
63.9908-1.35491.21085.5962.83495.9237-0.07140.142-0.10610.0706-0.24190.11920.0131-0.28060.29630.11590.0291-0.00030.1975-0.00090.1722-7.2408-30.6706-11.914
72.6413-0.340.33081.5796-0.02991.8922-0.0181-0.22140.13020.0702-0.09110.0037-0.1127-0.1490.1130.14870.01390.00650.2525-0.02910.2137-5.9139-27.9764-2.0795
80.67830.3162-1.67033.7083-1.63684.27070.1322-0.4046-0.11150.4358-0.2689-0.32920.05640.43560.14110.2843-0.034-0.0820.41380.04350.23018.5338-36.871812.5648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 22:48)A22 - 48
2X-RAY DIFFRACTION2chain 'A' and (resseq 49:61)A49 - 61
3X-RAY DIFFRACTION3chain 'A' and (resseq 62:103)A62 - 103
4X-RAY DIFFRACTION4chain 'A' and (resseq 104:125)A104 - 125
5X-RAY DIFFRACTION5chain 'A' and (resseq 126:139)A126 - 139
6X-RAY DIFFRACTION6chain 'A' and (resseq 140:159)A140 - 159
7X-RAY DIFFRACTION7chain 'A' and (resseq 160:199)A160 - 199
8X-RAY DIFFRACTION8chain 'A' and (resseq 200:228)A200 - 228

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