PDB-4km6: Human folate receptor alpha (FOLR1) at acidic pH, orthorhombic form

ID or keywords:

Entry

Database: PDB / ID: 4km6

Title

Human folate receptor alpha (FOLR1) at acidic pH, orthorhombic form

Components

Folate receptor alpha

Folate receptor 1

Keywords

MEMBRANE 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Singh, M. / Dann III, C.E.

Citation

Journal: 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

Deposition	May 8, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 2, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Jul 29, 2020	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 / _database_PDB_caveat.text / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4km6.cif.gz	97.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4km6.ent.gz	77.3 KB	Display	PDB format
PDBx/mmJSON format	4km6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/km/4km6 ftp://data.pdbj.org/pub/pdb/validation_reports/km/4km6	HTTPS FTP

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Related structure data

Related structure data	4km7C 4kmxC 4kmyC 4kmzC 4kn0C 4kn1C 4kn2C C: citing same article (ref.)
Similar structure data	5nnh-d 6qyf-d 7cmm-2 3tcj-d 5b60-d 4wpl-d 1im8-1 4tmd-d 3s4l-d 2ce4-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#53 - May 2004 Serpins similarity (2) #194 - Feb 2016 Designer Insulins similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #14 - Feb 2001 Insulin similarity (1) #222 - Jun 2018 Proteins and Nanoparticles similarity (1)

Deposited unit

A: Folate receptor alpha

hetero molecules

25 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	36.519, 63.339, 71.169
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

Folate receptor alpha /

Folate receptor 1 / FR-alpha / Adult folate-binding protein / FBP / Folate receptor 1 / Folate receptor / adult / KB ...

Mass: 24322.357 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: FOLR, FOLR1, FOLR2 / Plasmid: pSGHV0 / Cell line (production host): CHO / Production host:

Cricetulus griseus (Chinese hamster) / References: UniProt: P15328

#2: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#4: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.65 Å³/Da / Density % sol: 25.55 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 12 mg/mL co-purified with methotrexate in 0.1 M sodium citrate, , 35 % (v/v) jeffamine ED-2001 (MTX not present in structure), pH 5.5, Vapor diffusion, sitting drop, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 4.2.2 / Wavelength: 1 Å

Detector

Type: NOIR-1 / Detector: CCD / Date: Mar 2, 2011
Details: The NOIR-1 detector was built by E. Westbrook; 180 cm lens focused CCD

Radiation

Monochromator: SAGITALLY FOCUSED Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.55→50 Å / Num. obs: 24336 / % possible obs: 98.3 % / Redundancy: 5.7 % / R_merge(I) obs: 0.087 / Net I/σ(I): 10

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.55-1.58	4.5	0.495	1	86.8
1.58-1.61	4.8	0.456	1	90.9
1.61-1.64	5	0.427	1	94.5
1.64-1.67	5.3	0.429	1	97
1.67-1.71	5.5	0.372	1	99.1
1.71-1.75	5.7	0.338	1	99.9
1.75-1.79	5.9	0.32	1	99.9
1.79-1.84	5.9	0.262	1	99.9
1.84-1.89	6	0.242	1	100
1.89-1.95	6	0.218	1	100
1.95-2.02	6	0.179	1	100
2.02-2.1	5.9	0.165	1	100
2.1-2.2	6	0.142	1	100
2.2-2.32	6	0.13	1	99.8
2.32-2.46	6	0.113	1	100
2.46-2.65	6	0.096	1	99.9
2.65-2.92	6	0.078	1	99.8
2.92-3.34	5.9	0.058	1	99.8
3.34-4.21	5.9	0.045	1	99.5
4.21-50	5.6	0.038	1	98.6

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
DENZO		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→32.491 Å / Occupancy max: 1 / Occupancy min: 0.83 / SU ML: 0.19 / σ(F): 0 / Phase error: 20.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1999	1906	8.22 %
R_work	0.1684	-	-
obs	0.171	23197	93.9 %

Solvent computation

Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.912 Å² / k_sol: 0.428 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.8842 Å²	-0 Å²	0 Å²
2-	-	-4.5171 Å²	0 Å²
3-	-	-	9.4013 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→32.491 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1667	0	43	126	1836

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	1777
X-RAY DIFFRACTION	f_angle_d	1.163	2401
X-RAY DIFFRACTION	f_dihedral_angle_d	14.613	642
X-RAY DIFFRACTION	f_chiral_restr	0.081	239
X-RAY DIFFRACTION	f_plane_restr	0.007	309

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.55-1.5874	0.28	110	0.2323	1229	X-RAY DIFFRACTION	77
1.5874-1.6303	0.2579	115	0.2033	1325	X-RAY DIFFRACTION	84
1.6303-1.6783	0.2582	122	0.2059	1377	X-RAY DIFFRACTION	87
1.6783-1.7324	0.2411	133	0.1896	1482	X-RAY DIFFRACTION	91
1.7324-1.7944	0.2299	134	0.1827	1467	X-RAY DIFFRACTION	93
1.7944-1.8662	0.2315	134	0.1737	1511	X-RAY DIFFRACTION	94
1.8662-1.9511	0.2446	138	0.1708	1519	X-RAY DIFFRACTION	95
1.9511-2.054	0.2076	141	0.1649	1574	X-RAY DIFFRACTION	97
2.054-2.1826	0.2164	141	0.1602	1568	X-RAY DIFFRACTION	98
2.1826-2.3511	0.1913	144	0.1653	1607	X-RAY DIFFRACTION	99
2.3511-2.5876	0.2012	143	0.1747	1608	X-RAY DIFFRACTION	99
2.5876-2.9618	0.1951	146	0.1725	1624	X-RAY DIFFRACTION	99
2.9618-3.7308	0.1682	149	0.1498	1658	X-RAY DIFFRACTION	100
3.7308-32.4983	0.1759	156	0.1602	1742	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	4.2526	0.231	0.0659	1.3321	-2.0769	4.0583	0.0462	-0.0463	0.3784	0.0959	-0.0528	-0.3302	-0.2516	0.2435	-0.0169	0.1458	-0.0159	-0.0191	0.0743	-0.001	0.1931	5.4378	43.7735	37.0965
2	5.0839	-0.6046	0.5004	4.432	-1.4257	6.1364	-0.0708	0.7537	-0.5805	-0.7794	0.0103	-0.1542	0.2621	0.1605	-0.0178	0.2096	-0.0024	0.0171	0.1582	-0.0582	0.1505	2.6071	29.0825	27.1378
3	2.4274	0.628	-1.5517	3.997	-0.8922	2.951	0.0363	0.586	0.3545	-0.5272	-0.2862	-0.7431	-0.2565	0.6509	0.1669	0.2679	-0.0308	0.0535	0.276	0.0353	0.2582	9.4595	35.3347	29.0966
4	2.7947	-0.7635	-0.6483	1.5177	-1.0238	3.4917	-0.0107	0.0004	-0.1933	-0.1078	0.0065	0.0528	0.2069	-0.0569	0.0386	0.0236	0.018	-0.0062	0.0439	-0.0165	0.0663	6.7099	16.4358	39.3262
5	0.8064	0.2717	-0.7456	3.6215	0.0447	0.7382	0.0092	-0.0101	-0.0042	-0.063	0.0372	-0.0397	0.016	0.01	-0.048	0.0756	0.0053	-0.0234	0.1045	0.0072	0.0703	-1.5313	29.4372	42.2035
6	6.8029	0.7488	-0.8592	1.645	-0.1212	1.7812	-0.0375	-0.1349	0.2154	0.0999	0.0302	-0.0044	-0.0884	0.0991	0.0149	0.0986	0.0126	-0.0248	0.0735	0.0229	0.0914	8.0913	17.7292	47.371
7	1.058	0.0187	-0.9804	2.3163	-0.0719	0.9761	-0.0017	-0.0636	-0.0312	0.0822	-0.0646	-0.0563	0.0042	0.0435	0.0506	0.1071	0.0009	-0.0294	0.126	0.016	0.0763	-0.416	20.7701	50.8518
8	6.8788	-1.4664	-3.9244	4.6263	0.6796	6.8683	-0.2293	0.2524	-0.2374	0.0461	0.0021	0.2534	0.2027	-0.2988	0.2115	0.1075	-0.0084	-0.0254	0.087	0.0051	0.1513	-12.4018	32.2017	38.068
9	4.799	-0.5655	-1.6572	5.1404	1.7862	2.4517	0.1382	0.2253	0.1677	-0.3784	-0.0312	0.148	-0.1681	-0.2328	0.0192	0.1402	0.0223	-0.0388	0.1132	0.0381	0.1344	-10.6354	40.4649	37.1838

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 30:49)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 50:60)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 61:80)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 81:93)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 94:146)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 147:166)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 167:201)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 202:215)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 216:233)

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