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- PDB-4kn1: Human folate receptor beta (FOLR2) in complex with the antifolate... -

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Basic information

Entry
Database: PDB / ID: 4kn1
TitleHuman folate receptor beta (FOLR2) in complex with the antifolate aminopterin
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 / sperm-egg recognition / folic acid transport / 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 / sperm-egg recognition / folic acid transport / 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
Aminopterin / : / Folate receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)25,1947
Polymers24,0221
Non-polymers1,1726
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.075, 97.075, 98.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21A-458-

HOH

31A-483-

HOH

41A-507-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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 / Fragment: UNP residues 24-228
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: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 116 molecules

#3: Chemical ChemComp-04J / Aminopterin / N-(4-{[(2,4-diaminopteridin-6-yl)methyl]amino}benzoyl)-L-glutamic acid


Mass: 440.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N8O5
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Lithium sulfate, 0.1 M Tris-HCl pH 8.0, 20% (w/v) PEG 3350, 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: 1.2802 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 1, 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: 1.2802 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 12567 / % possible obs: 98.4 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.155 / Χ2: 0.779 / Net I/σ(I): 5.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3410.20.5985980.479197.4
2.34-2.3810.60.5476080.522197.6
2.38-2.4310.60.5856090.483197.6
2.43-2.4810.90.5646070.498197.1
2.48-2.5310.90.5126000.521198
2.53-2.5910.90.426150.551197.9
2.59-2.6610.80.3996070.601198.2
2.66-2.7310.80.3376100.684198.2
2.73-2.8110.90.3276140.701198.2
2.81-2.910.80.2956310.727198.3
2.9-310.80.2456140.832197.9
3-3.1210.80.2096150.998198.9
3.12-3.2610.70.1616281.039199.1
3.26-3.4410.70.1476321.066198.3
3.44-3.6510.60.1326311.008199.4
3.65-3.9310.60.1246420.857198.8
3.93-4.3310.40.1156480.996198.9
4.33-4.9510.20.1166500.947199.1
4.95-6.2410.10.0936701.007199.4
6.24-509.30.0787381.001198.8

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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: 2.301→48.538 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.824 / SU ML: 0.6 / σ(F): 1.33 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 1002 7.99 %
Rwork0.1875 --
obs0.1914 12543 98.42 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.032 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 102.88 Å2 / Biso mean: 36.1146 Å2 / Biso min: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.6381 Å20 Å20 Å2
2---4.6381 Å2-0 Å2
3---9.2762 Å2
Refinement stepCycle: LAST / Resolution: 2.301→48.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 75 111 1834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041797
X-RAY DIFFRACTIONf_angle_d0.8452431
X-RAY DIFFRACTIONf_chiral_restr0.063241
X-RAY DIFFRACTIONf_plane_restr0.003312
X-RAY DIFFRACTIONf_dihedral_angle_d13.469638
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3005-2.42180.26511370.20271587172497
2.4218-2.57350.30311380.23811595173398
2.5735-2.77220.30471410.22951610175198
2.7722-3.05120.28841410.2341622176399
3.0512-3.49260.25721430.18521645178899
3.4926-4.39980.21851460.15491678182499
4.3998-48.54830.17651560.17391804196099
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)
11.57550.41241.07643.3223-2.66815.99880.13310.1439-0.4758-0.19830.0482-0.31030.66310.1967-0.10040.26210.0605-0.05120.251-0.05010.28229.959-47.1728-11.4302
24.7233-0.9845-0.43448.23943.21242.7070.1697-0.122-0.790.4876-0.13880.75051.0161-1.0289-0.00450.2989-0.0629-0.03450.30590.04760.3333-3.7951-42.7493-2.5838
32.0579-0.58670.6242.9021.5493.5481-0.0064-0.2024-0.22050.2625-0.06330.01270.2013-0.01170.07140.2212-0.0476-0.03260.18760.07510.2354.7435-36.13863.1886
41.46031.91631.01654.5303-1.06436.8028-0.00470.014-0.1968-0.36460.0185-0.18890.2790.619-0.00110.15790.0427-0.01910.1733-0.02750.182915.3676-38.8343-9.7347
54.54350.35820.08884.16230.22047.51610.0208-0.07410.3034-0.2612-0.1272-0.0672-0.35610.03920.2010.18480.0288-0.02170.1869-0.0150.31163.7218-21.612-5.4972
65.7631-1.11251.79265.1013-0.23596.12670.0753-0.01950.05980.0873-0.044-0.4044-0.0770.25860.010.1607-0.0038-0.01910.1428-0.0190.158616.6686-28.41016.8827
70.72120.0290.27511.77240.64711.34310.1149-0.01180.08280.1574-0.06590.00930.08970.0497-0.05220.2337-0.0641-0.02190.22080.01080.272913.5956-23.9581-2.3691
82.5364-0.9838-2.91543.90210.13278.56530.05390.38270.13440.09030.12260.55440.1395-0.7733-0.14060.20780.0487-0.02710.3725-0.01070.3174-1.7699-33.0939-13.9047
97.54890.2854-5.60525.76450.61266.42780.03390.5113-0.0854-0.47230.0992-0.43220.1247-0.1428-0.07310.2730.0543-0.13330.2582-0.03610.20916.8522-37.2419-22.1679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 24:42)A24 - 42
2X-RAY DIFFRACTION2chain 'A' and (resseq 43:54)A43 - 54
3X-RAY DIFFRACTION3chain 'A' and (resseq 55:103)A55 - 103
4X-RAY DIFFRACTION4chain 'A' and (resseq 104:129)A104 - 129
5X-RAY DIFFRACTION5chain 'A' and (resseq 130:140)A130 - 140
6X-RAY DIFFRACTION6chain 'A' and (resseq 141:160)A141 - 160
7X-RAY DIFFRACTION7chain 'A' and (resseq 161:198)A161 - 198
8X-RAY DIFFRACTION8chain 'A' and (resseq 199:214)A199 - 214
9X-RAY DIFFRACTION9chain 'A' and (resseq 215:228)A215 - 228

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