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- PDB-4kmz: Human folate receptor beta (FOLR2) in complex with the folate -

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Basic information

Entry
Database: PDB / ID: 4kmz
TitleHuman folate receptor beta (FOLR2) in complex with the folate
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
FOLIC ACID / : / Folate receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Atomic model / Data collection ...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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _struct_conn.ptnr2_label_asym_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 20, 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)24,9625
Polymers24,0221
Non-polymers9404
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.861, 96.861, 98.337
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 53 molecules

#3: Chemical ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6
#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.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.4 M Ammonium phosphate diabasic, 0.1 M Hepes pH 7.5, 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: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 24, 2010
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: 2.3→50 Å / Num. obs: 12052 / % possible obs: 95.2 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.089 / Χ2: 0.868 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.348.60.4895230.576185.5
2.34-2.389.30.4245240.556187
2.38-2.439.60.55530.489188.2
2.43-2.4810.20.4455330.562187.4
2.48-2.5310.20.3535540.484190.1
2.53-2.5910.60.3515690.509192.2
2.59-2.6610.90.2985870.584194.4
2.66-2.7311.20.2716001.167197.7
2.73-2.8111.70.2576100.504197.9
2.81-2.911.90.1876130.509198.2
2.9-3120.1696210.577199.4
3-3.12120.1386250.576199.4
3.12-3.2611.90.116220.743199.4
3.26-3.44120.0996201.079198.7
3.44-3.6511.90.096271.318198.7
3.65-3.9311.90.0836321.946198.9
3.93-4.3311.80.0446321.154198.4
4.33-4.9511.70.0466471.005198.2
4.95-6.2411.60.0456521.34197.6
6.24-5010.60.0347081.021195.5

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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 4KMX

4kmx


Resolution: 2.3→48.43 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.769 / SU ML: 0.65 / σ(F): 1.33 / Phase error: 28.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 1203 10 %
Rwork0.2053 --
obs0.2108 12030 95.29 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.832 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 145.37 Å2 / Biso mean: 42.784 Å2 / Biso min: 25.54 Å2
Baniso -1Baniso -2Baniso -3
1--11.0032 Å20 Å20 Å2
2---11.0032 Å20 Å2
3---22.0063 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 62 50 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061757
X-RAY DIFFRACTIONf_angle_d0.932377
X-RAY DIFFRACTIONf_chiral_restr0.07234
X-RAY DIFFRACTIONf_plane_restr0.004306
X-RAY DIFFRACTIONf_dihedral_angle_d15.153622
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 (%)
2.3-2.39170.36381170.28391053117086
2.3917-2.50060.34261200.29781085120588
2.5006-2.63240.36541260.26081139126593
2.6324-2.79730.38161340.2531203133797
2.7973-3.01330.29821380.22531236137499
3.0133-3.31640.29291370.21321234137199
3.3164-3.79620.24631380.19821250138899
3.7962-4.78210.19831420.14871272141498
4.7821-48.44120.21851510.19951355150698
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)
10.0366-0.03930.04530.11510.04790.13360.2286-0.0836-0.4880.0541-0.03680.11770.44690.26540.0010.35470.0217-0.00410.3642-0.02240.463641.930836.354556.9304
20.379-0.1623-0.27710.12090.2080.3618-0.06130.0273-0.0146-0.139-0.0653-0.06440.01570.1119-00.32950.0124-0.04140.3184-0.07690.328543.732647.516446.3371
30.0494-0.0205-0.0360.01690.04190.0798-0.15150.0941-0.15680.1431-0.01220.15080.1223-0.222-0.00010.3567-0.0579-0.04610.3423-0.03140.388231.70543.4458.6468
40.02290.01350.00630.0522-0.03160.0184-0.001-0.10950.15420.3095-0.2308-0.15690.120.5134-0.00010.381-0.0442-0.02720.32990.00190.360143.410560.35256.4207
50.0507-0.03540.02570.0248-0.02630.0326-0.0067-0.1479-0.01230.3811-0.17380.1553-0.62170.03350.0010.4155-0.0299-0.07450.3594-0.03810.380434.754761.160944.3523
60.1307-0.12630.05490.1973-0.15190.10930.03410.12640.0821-0.40210.00470.0725-0.1772-0.1899-0.00010.32770.0474-0.08630.306-0.0350.347129.99458.199741.811
7-0.01340.0056-0.00210.027-0.08660.23920.13-0.030.0013-0.0698-0.102-0.17830.04380.091700.3234-0.0028-0.01070.3356-0.00230.318842.891854.029760.8045
80.0344-0.04120.00950.0426-0.00480.0496-0.0311-0.1532-0.11220.3376-0.00850.01460.32850.03790.00010.4511-0.0522-0.04910.42270.01290.376342.105545.966371.6501
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 151:178)A151 - 178
7X-RAY DIFFRACTION7chain 'A' and (resseq 179:215)A179 - 215
8X-RAY DIFFRACTION8chain 'A' and (resseq 216:227)A216 - 227

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