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- PDB-4km7: Human folate receptor alpha (FOLR1) at acidic pH, triclinic form -

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Basic information

Entry
Database: PDB / ID: 4km7
TitleHuman folate receptor alpha (FOLR1) at acidic pH, triclinic form
ComponentsFolate receptor alpha
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 / sperm-egg recognition / folic acid transport / 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 / sperm-egg recognition / folic acid transport / 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 / clathrin-coated vesicle / regulation of canonical Wnt signaling pathway / COPII-mediated vesicle transport / folic acid binding / axon regeneration / heart looping / folic acid metabolic process / tetrahydrofolate biosynthetic process / transport vesicle / COPI-mediated anterograde transport / 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 / Golgi membrane / external side of plasma membrane / endoplasmic reticulum membrane / cell surface / extracellular exosome / nucleus / membrane / 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: 1.801 Å
AuthorsKovach, A.R. / Wibowo, 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: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 alpha
B: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6608
Polymers48,6972
Non-polymers9636
Water7,927440
1
A: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8304
Polymers24,3481
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8304
Polymers24,3481
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.709, 55.384, 69.504
Angle α, β, γ (deg.)72.230, 86.950, 90.120
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Folate receptor alpha / 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.: 2 / 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
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / 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.: 4
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.: 440 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M Citrate, pH 4.5, 0.1 M LiCl, 17.5 % PEG 8000, 40% (v/v) 2,2,2-trifluoroethanol, Vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 18, 2006
Details: ANL-ECT, 210 mm x 210 mm active area 1.8 sec readout
RadiationMonochromator: SAGITALLY FOCUSED Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 43186 / % possible obs: 97.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Χ2: 1.092 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.833.40.1821591.061199.1
1.83-1.863.40.16922121.083197.8
1.86-1.93.50.16521331.104197.7
1.9-1.943.40.1521521.07198.5
1.94-1.983.40.13922271.08197.6
1.98-2.033.50.13121351.077198.4
2.03-2.083.50.1321491.105198.2
2.08-2.133.50.12422051.118198.8
2.13-2.23.50.12321471.148198.5
2.2-2.273.40.11721771.154198.7
2.27-2.353.50.11822051.207199.1
2.35-2.443.40.11521601.199198.9
2.44-2.553.50.10622171.154199.1
2.55-2.693.50.10921811.183198.9
2.69-2.863.50.10721651.188198.4
2.86-3.083.40.10221971.174198.4
3.08-3.393.50.0921621.007197.3
3.39-3.883.30.09121031.017197.3
3.88-4.882.80.08420550.934192.2
4.88-503.60.07320450.71192.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.801→28.095 Å / Occupancy max: 1 / Occupancy min: 0.67 / FOM work R set: 0.7913 / SU ML: 0.22 / σ(F): 0.08 / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 1980 4.63 %
Rwork0.222 --
obs0.2242 42731 96.58 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.76 Å2 / Biso mean: 17.7568 Å2 / Biso min: 2.47 Å2
Refinement stepCycle: LAST / Resolution: 1.801→28.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 58 440 3657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063346
X-RAY DIFFRACTIONf_angle_d1.0294521
X-RAY DIFFRACTIONf_chiral_restr0.082443
X-RAY DIFFRACTIONf_plane_restr0.005581
X-RAY DIFFRACTIONf_dihedral_angle_d15.0681193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8008-1.84580.27971380.22352804294293
1.8458-1.89570.31021230.23312843296694
1.8957-1.95140.29041520.23352897304996
1.9514-2.01440.29081360.22262896303297
2.0144-2.08640.27321460.22552950309697
2.0864-2.16990.28351480.22812954310298
2.1699-2.26860.30421340.23032953308798
2.2686-2.38820.28111430.23053010315398
2.3882-2.53770.30521420.22582904304698
2.5377-2.73350.27411480.23032994314298
2.7335-3.00830.26231430.2332953309698
3.0083-3.44290.25041440.21942941308598
3.4429-4.33510.22291400.19482897303796
4.3351-28.09840.26821430.22192755289892
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)
12.0326-0.8354-0.08052.42031.12444.0378-0.05730.20.1216-0.25-0.07640.4442-0.2145-0.5650.12810.1697-0.003-0.02170.21150.01150.15874.107334.7616-16.1897
24.0781-1.2281-0.44494.64352.36662.88950.02340.30520.3085-0.2155-0.1188-0.1155-0.45010.32110.03260.1529-0.0526-0.02270.12760.05530.15713.693537.6023-12.9706
31.8322-0.88520.66441.4266-0.8863.2873-0.0413-0.02090.18680.06860.0065-0.0724-0.14610.01870.04110.1003-0.0315-0.00720.0822-0.00730.121715.784831.1723-0.5598
43.32841.1187-2.67591.70940.08182.88210.04480.07320.2924-0.01950.0590.2634-0.1409-0.0507-0.080.1336-0.0038-0.01160.1131-0.00170.07112.182325.7905-11.7156
52.02770.25231.37230.2217-0.0591.65030.0922-0.2111-0.23510.05990.0555-0.08110.20650.0765-0.15950.10240.01060.00630.09970.01020.188216.560319.4676-7.1736
62.56080.25890.19592.566-0.44153.1446-0.0945-0.1724-0.07920.37460.08770.1685-0.06330.00010.01330.1720.01780.02690.10070.02440.09610.702225.95629.9048
71.4919-0.44521.06960.1343-0.45324.65330.0576-0.06590.00630.0019-0.00030.01530.2745-0.0475-0.05080.1342-0.0121-0.00480.0690.00630.160914.113516.5899-0.7038
84.81630.6854-0.51465.9034-0.83513.51760.00340.22590.0603-0.30260.2231-0.6819-0.38140.2318-0.17850.177-0.04750.03740.2209-0.03310.126720.030723.4905-18.1544
95.5135-0.61081.4714.2445-1.70617.92370.12850.466-0.2426-0.3084-0.04670.11050.26430.0998-0.07720.206-0.0034-0.00930.1406-0.01520.059810.454519.7194-23.4201
101.1803-1.6622-0.55462.90970.17862.2854-0.0869-0.30920.45950.23120.0451-0.6781-0.0660.44160.02510.1658-0.0287-0.03880.1895-0.03250.230129.59836.186627.5053
115.324.1201-0.05585.7319-1.41733.4494-0.0123-0.32030.42340.2297-0.00430.2027-0.4099-0.38080.01710.23160.04680.00440.1334-0.02280.146516.849710.628524.1161
120.77760.5631-0.79143.19641.69372.7915-0.07990.09660.1472-0.2770.1395-0.1048-0.3268-0.1532-0.03410.16030.04270.01390.07940.04020.124219.30016.28078.4642
137.63833.31315.75091.55122.29126.0480.0391-0.17440.32810.069-0.21180.11150.0256-0.04660.14140.11850.01930.00320.06630.01210.103715.27922.240115.6109
144.2475-0.4191-3.49392.4228-1.0393.66480.1028-0.08680.1753-0.0161-0.1155-0.22110.10730.01360.01610.1009-0.0137-0.01520.11370.01090.082830.2188-1.882522.2389
152.0924-0.61541.06211.8892-0.66532.85470.10490.0921-0.4332-0.10790.07230.11610.1751-0.1818-0.17420.1114-0.00480.00930.0651-0.00640.129415.53-8.266417.4933
166.3957-0.67190.32773.10551.97753.5485-0.2040.2193-0.3111-0.20280.21120.12350.1787-0.16430.02250.1631-0.0552-0.00090.09230.02830.103516.0694-5.59573.2414
174.37180.63311.58952.15252.07982.6577-0.17260.33190.2471-0.37120.2214-0.27920.1040.1508-0.04290.1567-0.03060.050.15910.00140.131924.93150.4526-0.8496
183.03930.9125-0.08281.0765-0.09052.96590.01010.1012-0.19180.1120.0074-0.02460.2508-0.067-0.00470.10890.02470.0140.0571-0.00320.093318.2861-11.070411.1775
194.3859-0.74630.70714.8284-0.15273.173-0.0897-0.19360.0310.2854-0.07170.1998-0.1539-0.15970.15070.128-0.00180.01550.13970.00260.074815.3321-5.233430.4959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 31:54)A31 - 54
2X-RAY DIFFRACTION2chain 'A' and (resseq 55:79)A55 - 79
3X-RAY DIFFRACTION3chain 'A' and (resseq 80:109)A80 - 109
4X-RAY DIFFRACTION4chain 'A' and (resseq 110:126)A110 - 126
5X-RAY DIFFRACTION5chain 'A' and (resseq 127:146)A127 - 146
6X-RAY DIFFRACTION6chain 'A' and (resseq 147:176)A147 - 176
7X-RAY DIFFRACTION7chain 'A' and (resseq 177:201)A177 - 201
8X-RAY DIFFRACTION8chain 'A' and (resseq 202:220)A202 - 220
9X-RAY DIFFRACTION9chain 'A' and (resseq 221:233)A221 - 233
10X-RAY DIFFRACTION10chain 'B' and (resseq 32:51)B32 - 51
11X-RAY DIFFRACTION11chain 'B' and (resseq 52:65)B52 - 65
12X-RAY DIFFRACTION12chain 'B' and (resseq 66:93)B66 - 93
13X-RAY DIFFRACTION13chain 'B' and (resseq 94:109)B94 - 109
14X-RAY DIFFRACTION14chain 'B' and (resseq 110:126)B110 - 126
15X-RAY DIFFRACTION15chain 'B' and (resseq 127:146)B127 - 146
16X-RAY DIFFRACTION16chain 'B' and (resseq 147:156)B147 - 156
17X-RAY DIFFRACTION17chain 'B' and (resseq 157:176)B157 - 176
18X-RAY DIFFRACTION18chain 'B' and (resseq 177:201)B177 - 201
19X-RAY DIFFRACTION19chain 'B' and (resseq 202:231)B202 - 231

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