[English] 日本語
Yorodumi
- PDB-4kmy: Human folate receptor beta (FOLR2) at neutral pH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kmy
TitleHuman folate receptor beta (FOLR2) at neutral pH
ComponentsFolate receptor beta
KeywordsMEMBRANE PROTEIN / Folate Receptor Beta / FOLR2 / GPI-anchor membrane receptor / Folic acid / folates / 5-methyltetrahydrofolate / antifolates / folate-conjugates / 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
: / Folate receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 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 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Folate receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2823
Polymers24,0221
Non-polymers2602
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.026, 75.026, 97.188
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#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
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: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / 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.: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.0 M Ammonium citrate tribasic, pH 7.0, 0.1 M Bis-Tris Propane, pH 7.0, Vapor diffusion, sitting drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 2, 2011
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: 1.79→50 Å / Num. obs: 28977 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.093 / Χ2: 0.875 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.79-1.833.70.45514700.68199.7
1.83-1.864.20.41514210.547199.9
1.86-1.94.50.39414190.6199.9
1.9-1.944.70.32614460.58199.9
1.94-1.984.70.27214600.718199.9
1.98-2.034.70.23714480.736199.9
2.03-2.084.80.21514340.791199.9
2.08-2.134.80.17614340.998199.9
2.13-2.24.80.1514561.018199.9
2.2-2.274.70.14514380.7821100
2.27-2.354.80.13114361.0161100
2.35-2.444.80.12514561.0781100
2.44-2.554.80.11514571.0381100
2.55-2.694.80.11214430.9071100
2.69-2.864.80.1114451.0131100
2.86-3.084.80.10914551.0021100
3.08-3.394.80.09714511.0421100
3.39-3.884.80.08514510.9611100
3.88-4.884.80.06914640.867199.8
4.88-504.70.07414930.97199.8

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KMZ

4kmz


Resolution: 1.795→37.513 Å / Occupancy max: 1 / Occupancy min: 0.6 / FOM work R set: 0.8952 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 17.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 1199 4.14 %
Rwork0.1638 --
obs0.1649 28939 99.84 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.735 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 85.91 Å2 / Biso mean: 32.0993 Å2 / Biso min: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.3435 Å2-0 Å2-0 Å2
2--0.3435 Å2-0 Å2
3----0.6871 Å2
Refinement stepCycle: LAST / Resolution: 1.795→37.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 15 164 1846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091745
X-RAY DIFFRACTIONf_angle_d1.1132357
X-RAY DIFFRACTIONf_chiral_restr0.084232
X-RAY DIFFRACTIONf_plane_restr0.006306
X-RAY DIFFRACTIONf_dihedral_angle_d11.821624
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 (%)
1.7953-1.86720.24891510.21233035318699
1.8672-1.95220.24811340.19130713205100
1.9522-2.05510.22471360.17530593195100
2.0551-2.18380.19711280.160630743202100
2.1838-2.35240.21121300.16631263256100
2.3524-2.58910.20341360.178630533189100
2.5891-2.96360.23051200.178130933213100
2.9636-3.73330.18451440.158930943238100
3.7333-37.52120.1561200.14731353255100
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)
12.78351.00170.21173.523-1.00424.31640.0397-0.2692-0.4885-0.0592-0.1503-0.330.64710.13630.11940.29990.05010.01650.26190.05110.31419.5282-47.59971.5277
22.56-0.47220.13425.61-0.49773.5335-0.0249-0.00590.09480.0262-0.0552-0.66450.21160.56570.07380.16050.02660.00960.27510.00860.288815.1516-39.1754-1.9076
32.3608-0.07351.07080.8250.02431.5748-0.02190.20850.0841-0.2469-0.0942-0.09120.03720.04690.10740.20690.01180.02990.2387-0.00040.21485.423-32.8741-10.8319
42.96650.5441-0.04073.07131.53354.29970.0880.0499-0.3047-0.1402-0.22070.19510.6314-0.4520.10790.3351-0.0520.00450.25350.02560.244-1.7025-46.13661.4386
52.73110.39820.10335.5022-3.1374.4938-0.004-0.50080.60.6866-0.1333-0.0929-0.5551-0.04220.14650.209-0.0065-0.03150.2679-0.08830.30261.8392-25.06464.1939
63.9908-1.35491.21085.5962.83495.9237-0.07140.142-0.10610.0706-0.24190.11920.0131-0.28060.29630.11590.0291-0.00030.1975-0.00090.1722-7.2408-30.6706-11.914
72.6413-0.340.33081.5796-0.02991.8922-0.0181-0.22140.13020.0702-0.09110.0037-0.1127-0.1490.1130.14870.01390.00650.2525-0.02910.2137-5.9139-27.9764-2.0795
80.67830.3162-1.67033.7083-1.63684.27070.1322-0.4046-0.11150.4358-0.2689-0.32920.05640.43560.14110.2843-0.034-0.0820.41380.04350.23018.5338-36.871812.5648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 22:48)A22 - 48
2X-RAY DIFFRACTION2chain 'A' and (resseq 49:61)A49 - 61
3X-RAY DIFFRACTION3chain 'A' and (resseq 62:103)A62 - 103
4X-RAY DIFFRACTION4chain 'A' and (resseq 104:125)A104 - 125
5X-RAY DIFFRACTION5chain 'A' and (resseq 126:139)A126 - 139
6X-RAY DIFFRACTION6chain 'A' and (resseq 140:159)A140 - 159
7X-RAY DIFFRACTION7chain 'A' and (resseq 160:199)A160 - 199
8X-RAY DIFFRACTION8chain 'A' and (resseq 200:228)A200 - 228

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more