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- PDB-4kmx: Human folate receptor alpha (FOLR1) at acidic pH, hexagonal form -

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Basic information

Entry
Database: PDB / ID: 4kmx
TitleHuman folate receptor alpha (FOLR1) at acidic pH, hexagonal form
ComponentsFolate receptor alphaFolate receptor 1
KeywordsMEMBRANE PROTEIN / Folate Receptor Alpha / FOLR1 / folate receptor / Folic acid / folates / 5-methyltetrahydrofolate / antifolates / folate-conjugates / GPI-anchored protein on eukaryotic membrane / TRANSPORT PROTEIN
Function / homology
Function and homology information


cellular response to folic acid / neural crest cell migration involved in heart formation / folic acid receptor activity / folic acid transport / sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / pharyngeal arch artery morphogenesis / cardiac neural crest cell migration involved in outflow tract morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / anterior neural tube closure ...cellular response to folic acid / neural crest cell migration involved in heart formation / folic acid receptor activity / folic acid transport / sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / pharyngeal arch artery morphogenesis / cardiac neural crest cell migration involved in outflow tract morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / anterior neural tube closure / Cargo concentration in the ER / regulation of canonical Wnt signaling pathway / COPII-mediated vesicle transport / axon regeneration / clathrin-coated vesicle / folic acid binding / folic acid metabolic process / heart looping / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis / brush border membrane / ER to Golgi transport vesicle membrane / signaling receptor activity / basolateral plasma membrane / cell adhesion / endosome / apical plasma membrane / external side of plasma membrane / Golgi membrane / endoplasmic reticulum membrane / cell surface / extracellular exosome / membrane / nucleus / plasma membrane
Similarity search - Function
Folate receptor / Folate receptor-like / Folate receptor family
Similarity search - Domain/homology
: / Folate receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / 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_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / 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.occupancy / _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 / _pdbx_struct_conn_angle.ptnr2_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2155
Polymers24,3481
Non-polymers8664
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.193, 99.193, 56.869
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Folate receptor alpha / Folate receptor 1 / FR-alpha / Adult folate-binding protein / FBP / Folate receptor 1 / Folate receptor / adult / KB ...FR-alpha / Adult folate-binding protein / FBP / Folate receptor 1 / Folate receptor / adult / KB cells FBP / Ovarian tumor-associated antigen MOv18


Mass: 24348.438 Da / Num. of mol.: 1 / Fragment: UNP residues 28-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOLR1 / Plasmid: pFASTBAC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P15328

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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

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Non-polymers , 3 types, 197 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.35 Å3/Da / Density % sol: 63.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Citrate, pH 4.5, 0.1 M LiCl, 17.5 % PEG 8000, Vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: APS-1/SBC-1 / Detector: CCD / Date: Mar 1, 1996
Details: THE APS-1/SBC-1 AND THE SBC-2 WERE TWO DIFFERENT DETECTORS WITH THE SBC-2 BEING A NEWER VERSION
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: 2.2→30 Å / Num. obs: 15749 / % possible obs: 96.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.240.574190.4
2.24-2.280.541194.2
2.28-2.320.506197.7
2.32-2.370.487197.2
2.37-2.420.4391100
2.42-2.480.398197.2
2.48-2.540.324199.7
2.54-2.610.274197.4
2.61-2.680.237198.4
2.68-2.770.205198.4
2.77-2.870.184196.7
2.87-2.990.155197.1
2.99-3.120.131197.4
3.12-3.290.091197
3.29-3.490.074196.3
3.49-3.760.06195.4
3.76-4.140.048195.9
4.14-4.730.045193.8
4.73-5.960.042195.2
5.96-300.038192.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.635 Å / Occupancy max: 1 / Occupancy min: 0.83 / SU ML: 0.32 / σ(F): 1.93 / Phase error: 20.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 791 5.02 %
Rwork0.1659 --
obs0.168 15747 96.49 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.201 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.788 Å20 Å20 Å2
2---4.788 Å2-0 Å2
3---9.5761 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 54 195 1876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041749
X-RAY DIFFRACTIONf_angle_d0.8522365
X-RAY DIFFRACTIONf_dihedral_angle_d13.142624
X-RAY DIFFRACTIONf_chiral_restr0.067237
X-RAY DIFFRACTIONf_plane_restr0.004301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.33790.2771340.23372397X-RAY DIFFRACTION95
2.3379-2.51830.26061490.20592515X-RAY DIFFRACTION99
2.5183-2.77160.24911340.17152526X-RAY DIFFRACTION98
2.7716-3.17220.20911200.15162520X-RAY DIFFRACTION97
3.1722-3.99490.17071270.13612491X-RAY DIFFRACTION96
3.9949-28.6370.18561270.16962507X-RAY DIFFRACTION94
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)
11.8465-0.8755-0.64081.81050.95221.70270.0658-0.07810.35160.15620.1428-0.42290.19760.034-0.16930.239-0.0084-0.01020.2883-0.07940.201531.629567.0841-1.3423
21.7429-1.5461-0.47131.73440.63521.8009-0.5162-0.48830.56940.38640.5924-0.72740.15830.4152-0.15290.23640.0353-0.05860.2656-0.02880.38626.470277.27636.3797
32.5684-1.3994-0.84261.33270.85110.5746-0.2926-0.8413-0.35950.53910.3539-0.2576-0.26040.20.04230.29180.10270.04930.26420.03460.266617.617973.990613.9153
43.03950.1922-0.51721.453-0.93761.4253-0.2112-0.3655-0.65640.710.05140.07710.478-0.05520.28670.36240.05470.10590.23820.06930.34498.096470.643512.0385
53.47970.7401-1.32175.6417-1.59232.9440.0955-0.7975-1.13850.49250.31680.23530.30860.10280.06450.30060.0810.01830.30340.12180.38216.526270.155713.7509
62.9006-0.2934-1.48162.3604-0.15140.76030.0959-0.7998-0.06030.061-0.1622-0.1253-0.11630.19180.03680.2576-0.00120.02030.3355-0.00650.16848.580485.821510.8942
72.6314-0.50541.92513.10.64542.821-0.1379-0.4453-0.30860.1558-0.15850.54010.0905-0.58190.1590.2310.0360.06310.2201-0.01870.2147-3.46686.52333.8875
84.8896-1.00061.22710.4999-0.25750.61450.1507-0.3325-0.67830.24980.02560.24860.1314-0.1077-0.10650.23470.01080.01590.17180.02440.27945.050376.9624.3016
90.4561-0.1505-0.19362.73940.09621.21990.00070.0256-0.08520.0326-0.0536-0.4453-0.17450.1539-0.0070.22350.01250.00020.2244-0.03790.255920.683580.21260.7139
100.87520.5510.65610.9729-0.30052.7931-0.0020.5232-0.68280.21640.1214-0.1302-0.16120.2176-0.30510.22020.03590.02540.2866-0.12050.278915.912377.0148-4.8115
110.3359-0.74410.02871.98020.45141.2680.2660.4316-1.2465-0.27360.06040.5970.3402-0.22410.13790.2869-0.0153-0.06790.2317-0.13710.47230.599673.2552-7.0505
122.1997-0.94930.55661.46880.67711.15790.00790.06030.0229-0.1295-0.060.1075-0.1436-0.00370.0620.22790.0175-0.03080.1705-0.00260.14721.577489.239-3.7244
131.5258-0.06150.16532.5014-0.44350.1185-0.05020.1898-0.2162-0.5078-0.06250.2091-0.43140.4457-0.03350.29210.0073-0.01150.299-0.0220.123311.210578.9208-7.8073
142.5855-1.31980.42440.84950.30170.5712-0.0258-0.0793-1.6340.01120.06660.21880.135-0.1170.19070.236-0.0066-0.02480.128-0.09540.52119.904765.5788-3.4599
151.7344-1.0510.06691.2175-0.14933.37260.1399-0.1827-0.6616-0.2950.38690.53190.39420.43020.58730.29090.0962-0.03350.2482-0.02890.502318.152363.974-2.0245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 28:33)
2X-RAY DIFFRACTION2chain 'A' and (resseq 34:43)
3X-RAY DIFFRACTION3chain 'A' and (resseq 44:54)
4X-RAY DIFFRACTION4chain 'A' and (resseq 55:60)
5X-RAY DIFFRACTION5chain 'A' and (resseq 61:68)
6X-RAY DIFFRACTION6chain 'A' and (resseq 76:85)
7X-RAY DIFFRACTION7chain 'A' and (resseq 86:93)
8X-RAY DIFFRACTION8chain 'A' and (resseq 94:109)
9X-RAY DIFFRACTION9chain 'A' and (resseq 110:126)
10X-RAY DIFFRACTION10chain 'A' and (resseq 127:135)
11X-RAY DIFFRACTION11chain 'A' and (resseq 136:145)
12X-RAY DIFFRACTION12chain 'A' and (resseq 146:191)
13X-RAY DIFFRACTION13chain 'A' and (resseq 192:201)
14X-RAY DIFFRACTION14chain 'A' and (resseq 202:215)
15X-RAY DIFFRACTION15chain 'A' and (resseq 216:233)

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