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- PDB-4lrh: Crystal structure of human folate receptor alpha in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4lrh
TitleCrystal structure of human folate receptor alpha in complex with folic acid
ComponentsFolate receptor alpha
KeywordsFolate Binding Protein / folate receptor-alpha / folic acid / cysteine-rich glycoprotein
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 / clathrin-coated vesicle / axon regeneration / folic acid binding / heart looping / folic acid metabolic process / 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
FOLIC ACID / Folate receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsKe, J. / Chen, C. / Zhou, X.E. / Yi, W. / Brunzelle, J.S. / Li, J. / Young, E.-L. / Xu, H.E. / Melcher, K.
CitationJournal: Nature / Year: 2013
Title: Structural basis for molecular recognition of folic acid by folate receptors.
Authors: Chen, C. / Ke, J. / Zhou, X.E. / Yi, W. / Brunzelle, J.S. / Li, J. / Yong, E.L. / Xu, H.E. / Melcher, K.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJul 31, 2013ID: 4KEO
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Apr 8, 2015Group: Structure summary
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_auth_seq_id / _struct_conn.ptnr1_label_asym_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

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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
C: Folate receptor alpha
D: Folate receptor alpha
E: Folate receptor alpha
F: Folate receptor alpha
G: Folate receptor alpha
H: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,74938
Polymers204,3518
Non-polymers8,39830
Water3,531196
1
A: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6495
Polymers25,5441
Non-polymers1,1054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6495
Polymers25,5441
Non-polymers1,1054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4284
Polymers25,5441
Non-polymers8843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6495
Polymers25,5441
Non-polymers1,1054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6495
Polymers25,5441
Non-polymers1,1054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6495
Polymers25,5441
Non-polymers1,1054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4284
Polymers25,5441
Non-polymers8843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Folate receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6495
Polymers25,5441
Non-polymers1,1054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.021, 144.589, 216.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.38387, 0.91914, 0.088463), (-0.92025, 0.388697, -0.045336), (-0.076055, -0.064005, 0.995047)-51.55357, 64.11692, -8.15705

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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: 25543.855 Da / Num. of mol.: 8 / Fragment: Folate receptor alpha
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOLR1, FOLR / Cell line (production host): mammalian cell line / Production host: Homo sapiens (human) / References: UniProt: P15328
#2: Chemical
ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H19N7O6
#3: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 22
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.: 196 / 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: 3.36 Å3/Da / Density % sol: 63.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: PEG 2000,potassium sodium tartrate, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 71563 / Num. obs: 70984 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.1 % / Rmerge(I) obs: 0.15
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 1.231 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXSphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementResolution: 2.8→49 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 143
RfactorNum. reflection% reflection
Rfree0.2672 5716 8.1 %
Rwork0.2274 64269 -
obs-69985 99.3 %
Solvent computationBsol: 38.1884 Å2
Displacement parametersBiso max: 135.18 Å2 / Biso mean: 68.9391 Å2 / Biso min: 10.53 Å2
Baniso -1Baniso -2Baniso -3
1--2.775 Å20 Å20 Å2
2--1.252 Å20 Å2
3---1.522 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13568 0 564 196 14328
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.161
X-RAY DIFFRACTIONc_mcbond_it1.2271.5
X-RAY DIFFRACTIONc_scbond_it1.8452
X-RAY DIFFRACTIONc_mcangle_it2.1282
X-RAY DIFFRACTIONc_scangle_it2.9172.5
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 (%)
2.8-2.90.41015420.38146127666995.8
2.9-3.020.36595520.33026385693799.9
3.02-3.150.36345490.29956418696799.9
3.15-3.320.31095450.268864126957100
3.32-3.530.30555810.255164186999100
3.53-3.80.35435810.33646305688698.3
3.8-4.180.26495560.2086426698299.5
4.18-4.790.20665760.159964937069100
4.79-6.030.2056100.172565357145100
6.03-490.22996240.18826750737499.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top
X-RAY DIFFRACTION6nag_xplor_par.txtnag_xplor_top.txt
X-RAY DIFFRACTION7fol_xplor_par2.txtfol_xplor_top2.txt

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