[English] 日本語
Yorodumi
- PDB-4km7: Human folate receptor alpha (FOLR1) at acidic pH, triclinic form -

+
Open data


ID or keywords:

Loading...

-
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 / 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
: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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://pdbjlvh1.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