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- PDB-4kn2: Human folate receptor beta (FOLR2) in complex with antifolate pem... -

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Basic information

Entry
Database: PDB / ID: 4kn2
TitleHuman folate receptor beta (FOLR2) in complex with antifolate pemetrexed
ComponentsFolate receptor beta
KeywordsMEMBRANE PROTEIN / Folate Receptor Beta / FOLR2 / folate receptor / Folic acid / folates / 5-methyltetrahydrofolate / antifolates / folate-conjugates / GPI-anchored protein on eukaryotic membrane / 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
: / Chem-LYA / Folate receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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
B: Folate receptor beta
C: Folate receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,23515
Polymers72,0663
Non-polymers2,17012
Water2,072115
1
A: Folate receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7455
Polymers24,0221
Non-polymers7234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Folate receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7455
Polymers24,0221
Non-polymers7234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Folate receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7455
Polymers24,0221
Non-polymers7234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.443, 97.443, 348.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-407-

HOH

21B-426-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )
21chain B and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )
31chain C and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )A25 - 55
121chain A and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )A57 - 73
131chain A and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )A75 - 112
141chain A and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )A118 - 226
211chain B and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )B25 - 55
221chain B and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )B57 - 73
231chain B and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )B75 - 112
241chain B and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )B118 - 226
311chain C and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )C25 - 55
321chain C and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )C57 - 73
331chain C and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )C75 - 112
341chain C and (resseq 25:55 or resseq 57:73 or resseq 75:112 or resseq 118:226 )C118 - 226

NCS oper:
IDCodeMatrixVector
1given(0.479575, 0.014846, -0.877375), (-0.017043, 0.999826, 0.007603), (0.877335, 0.011307, 0.479745)38.046398, -16.2132, 21.246099
2given(0.503626, 0.018325, -0.863728), (0.023008, -0.999705, -0.007794), (-0.863616, -0.015947, -0.503899)37.180599, 64.9562, 66.182404

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#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.: 3
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
#4: 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.: 3
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

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Non-polymers , 4 types, 124 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-LYA / 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID / LY231514


Mass: 427.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H21N5O6 / Comment: medication, chemotherapy*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 1.5 M Ammonium phosphate dibasc, 0.1 M Tris pH 8.5, 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: 0.9184 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(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26536 / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.113 / Χ2: 0.696 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.648.20.67513170.3791100
2.64-2.698.30.56812620.4661100
2.69-2.748.30.55713080.4041100
2.74-2.88.30.47913200.3941100
2.8-2.868.30.42912920.4251100
2.86-2.938.30.3713070.4271100
2.93-38.20.30412980.4881100
3-3.088.30.26913000.4731100
3.08-3.178.20.22113260.5461100
3.17-3.288.20.17713070.6291100
3.28-3.398.20.17112990.7191100
3.39-3.538.20.14813300.9641100
3.53-3.698.20.11113140.8651100
3.69-3.888.20.09713261.0031100
3.88-4.138.10.08213220.811100
4.13-4.458.10.07413491.0081100
4.45-4.898.10.0613470.971100
4.89-5.680.05813450.9061100
5.6-7.057.90.0613871.062199.7
7.05-507.30.04714800.978199.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KMZ

4kmz


Resolution: 2.6→48.721 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.841 / SU ML: 0.76 / σ(F): 0 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1341 5.06 %
Rwork0.1937 --
obs0.1962 26486 99.86 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.37 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 122.72 Å2 / Biso mean: 47.5735 Å2 / Biso min: 14.15 Å2
Baniso -1Baniso -2Baniso -3
1-4.3539 Å20 Å2-0 Å2
2--4.3539 Å2-0 Å2
3----8.7079 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 141 115 5077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085154
X-RAY DIFFRACTIONf_angle_d1.0676996
X-RAY DIFFRACTIONf_chiral_restr0.08686
X-RAY DIFFRACTIONf_plane_restr0.004907
X-RAY DIFFRACTIONf_dihedral_angle_d13.6151796
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1565X-RAY DIFFRACTIONPOSITIONAL0.04
12B1565X-RAY DIFFRACTIONPOSITIONAL0.04
13C1531X-RAY DIFFRACTIONPOSITIONAL0.036
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.68970.30221290.244924432572100
2.6897-2.79740.30551230.233424962619100
2.7974-2.92470.26171400.228924622602100
2.9247-3.07890.28451200.213824752595100
3.0789-3.27180.27231330.195925032636100
3.2718-3.52430.22941450.198324852630100
3.5243-3.87880.22251360.184725002636100
3.8788-4.43980.22651550.159625112666100
4.4398-5.59240.21021300.175725502680100
5.5924-48.73010.25821300.20612720285099
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)
12.9651-1.13670.51524.41690.58122.5758-0.12650.45590.1552-0.4033-0.0785-0.7495-0.03830.95550.17820.2810.01280.06230.79560.06290.359144.698216.193625.7118
21.9113-0.33640.26932.1587-0.5460.84010.01470.1592-0.4533-0.3595-0.0962-0.20130.27370.39770.05820.18060.24140.10650.51950.02610.328534.15855.359629.1735
31.8852-1.2042-0.49564.01210.79281.0852-0.1327-0.28350.1680.29030.0418-0.68930.19440.5163-0.01440.15740.01530.02080.74830.10340.433443.566517.525237.7682
42.03752.926-0.31274.237-0.71221.8329-0.1543-0.00640.41890.12620.3250.32980.0132-0.53970.05220.11470.16910.05230.44870.00470.353123.053915.118435.9947
51.03041.1365-1.47186.66944.36818.73330.0111-0.3234-0.1010.03730.27590.2673-0.26280.0267-0.24910.2870.12540.02980.34810.13490.404326.60943.058443.7288
66.3134-1.7837-4.40971.7687-0.5836.3583-0.1554-0.5797-1.1432-0.0726-0.4544-0.52520.38190.9010.57770.33510.15440.01570.60990.12930.440435.6091-2.351946.3358
71.1440.43410.54883.6439-0.67961.4519-0.0773-0.02180.01-0.05380.01650.2534-0.0510.0250.04550.16290.08630.04640.45070.02770.288627.455417.0936.1317
82.38793.71623.99768.92796.77069.9162-0.13630.86970.6738-0.79240.1252-0.0647-0.90630.04470.04770.26310.08560.02440.60770.18410.355535.21829.45729.1444
92.56690.1134-0.33685.0565-0.4181.88540.46630.6845-0.0468-0.4655-0.4144-0.202-0.16150.0912-0.02940.25690.169-0.01550.4483-0.01670.25386.544932.5553-3.4497
102.1753-0.1928-0.15612.2132-0.3021.51680.07980.3516-0.1312-0.191-0.16290.09340.38420.03670.06910.12210.2731-0.00660.2395-0.17130.22883.653821.8872.5699
113.3676-1.28880.29751.98020.74680.5843-0.1221-0.1731-0.3774-0.0723-0.0433-0.16350.50010.10250.16240.24230.1349-0.01740.2595-0.03960.18695.939221.140112.9483
122.56390.29360.00756.76670.73143.78740.0830.0797-0.7992-0.24470.003-0.92620.35240.9684-0.02610.33270.16470.07140.4241-0.06210.352716.214434.23913.4785
134.95882.5935-0.05778.1917-4.14852.4854-0.0134-0.43660.28310.92060.29470.2592-0.669-0.7693-0.26860.36320.06660.07110.3831-0.05910.2125.210831.2720.4707
144.64044.44630.11198.2934-1.58494.34760.1478-0.2938-0.24880.62680.2961-0.3761-0.5873-0.1876-0.40380.39150.16680.00560.25160.01760.248413.902819.363120.9645
153.8413-2.34512.09363.4594-0.48577.44490.19820.26740.0443-0.3615-0.0437-0.21810.47490.484-0.11580.21640.11730.02410.2939-0.00620.245120.617614.118214.281
161.2288-0.36960.33942.6014-0.41012.7053-0.0971-0.20090.09880.3290.11280.2617-0.189-0.1312-0.00370.18980.07340.03740.3028-0.02840.25957.413233.308916.6842
173.39431.9443-1.52541.98070.96914.81730.0328-0.16630.64780.08150.19140.501-0.6893-0.5164-0.04160.34510.18550.01460.26180.00880.43254.814845.69436.6216
184.50532.20481.60616.9921-0.82161.6344-0.01880.71730.57-0.6453-0.4438-0.89530.12760.36420.19420.2634-0.00390.06890.70070.11970.530337.614349.542414.2825
193.9495-4.1019-6.11537.23975.45689.73920.00320.62070.61730.24430.3245-1.13540.2446-0.4412-0.34220.2925-0.1008-0.05570.53760.12720.515337.482652.726723.4968
204.5837-1.04650.21.47050.90262.0399-0.01970.11120.5931-0.0702-0.0635-0.5371-0.61550.40010.06580.3482-0.08660.00030.41950.15890.490126.594262.124221.2668
218.29893.4047-1.81476.63171.79962.2574-0.27540.20990.1981-0.99480.0076-0.0762-0.10250.2610.23750.32920.02710.07250.33410.08820.313726.609648.08949.6258
227.0691-5.0366-3.69155.12635.24526.378-0.3866-1.0298-0.33390.64160.34910.12640.62760.24840.07880.3367-0.0640.07510.42940.09090.309817.897750.301427.7667
235.7814-2.73610.74646.28322.86782.3255-0.28750.32810.521-0.13710.03590.1352-0.2018-0.09750.21830.26410.0129-0.02370.30840.13720.342213.978465.855515.3047
242.933-1.83840.47024.8075-0.21011.64590.155-0.0820.0055-0.07530.00750.04140.0820.2068-0.16360.146-0.0001-0.00330.32440.04920.264619.955548.148623.92
254.09531.4371-0.58827.04683.34748.6747-0.1231-0.5727-0.095-0.1089-0.1433-0.47570.8130.14040.01210.24820.07040.02150.49460.16790.283230.425336.353421.0147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 25:48)A25 - 48
2X-RAY DIFFRACTION2chain 'A' and (resseq 49:103)A49 - 103
3X-RAY DIFFRACTION3chain 'A' and (resseq 104:125)A104 - 125
4X-RAY DIFFRACTION4chain 'A' and (resseq 126:140)A126 - 140
5X-RAY DIFFRACTION5chain 'A' and (resseq 141:150)A141 - 150
6X-RAY DIFFRACTION6chain 'A' and (resseq 151:170)A151 - 170
7X-RAY DIFFRACTION7chain 'A' and (resseq 171:214)A171 - 214
8X-RAY DIFFRACTION8chain 'A' and (resseq 215:226)A215 - 226
9X-RAY DIFFRACTION9chain 'B' and (resseq 25:48)B25 - 48
10X-RAY DIFFRACTION10chain 'B' and (resseq 49:79)B49 - 79
11X-RAY DIFFRACTION11chain 'B' and (resseq 80:103)B80 - 103
12X-RAY DIFFRACTION12chain 'B' and (resseq 104:125)B104 - 125
13X-RAY DIFFRACTION13chain 'B' and (resseq 126:140)B126 - 140
14X-RAY DIFFRACTION14chain 'B' and (resseq 141:150)B141 - 150
15X-RAY DIFFRACTION15chain 'B' and (resseq 151:170)B151 - 170
16X-RAY DIFFRACTION16chain 'B' and (resseq 171:214)B171 - 214
17X-RAY DIFFRACTION17chain 'B' and (resseq 215:226)B215 - 226
18X-RAY DIFFRACTION18chain 'C' and (resseq 25:48)C25 - 48
19X-RAY DIFFRACTION19chain 'C' and (resseq 49:61)C49 - 61
20X-RAY DIFFRACTION20chain 'C' and (resseq 62:103)C62 - 103
21X-RAY DIFFRACTION21chain 'C' and (resseq 104:125)C104 - 125
22X-RAY DIFFRACTION22chain 'C' and (resseq 126:140)C126 - 140
23X-RAY DIFFRACTION23chain 'C' and (resseq 141:170)C141 - 170
24X-RAY DIFFRACTION24chain 'C' and (resseq 171:214)C171 - 214
25X-RAY DIFFRACTION25chain 'C' and (resseq 215:225)C215 - 225

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