[English] 日本語
Yorodumi
- PDB-4lij: Crystal structure of a far upstream element (FUSE) binding protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lij
TitleCrystal structure of a far upstream element (FUSE) binding protein 1 (FUBP1) from Homo sapiens at 1.95 A resolution
ComponentsFar upstream element-binding protein 1
KeywordsRNA BINDING PROTEIN / KH domain / PF00013 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / RNA-BINDING PROTEIN / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


single-stranded DNA binding / regulation of gene expression / mRNA binding / positive regulation of gene expression / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / : / : / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. ...: / : / : / : / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Far upstream element-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a far upstream element (FUSE) binding protein 1 (FUBP1) from Homo sapiens at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology
History
DepositionJul 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Structure summary / Category: software / struct_keywords
Item: _software.classification / _software.name / _struct_keywords.text
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Far upstream element-binding protein 1
B: Far upstream element-binding protein 1
C: Far upstream element-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9435
Polymers29,7533
Non-polymers1902
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Far upstream element-binding protein 1
B: Far upstream element-binding protein 1
C: Far upstream element-binding protein 1
hetero molecules

A: Far upstream element-binding protein 1
B: Far upstream element-binding protein 1
C: Far upstream element-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,88610
Polymers59,5066
Non-polymers3804
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9960 Å2
ΔGint-77 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.810, 86.810, 84.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-700-

PO4

21A-251-

HOH

31A-275-

HOH

41A-280-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TRIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Far upstream element-binding protein 1 / FBP / FUSE-binding protein 1 / DNA helicase V / hDH V


Mass: 9917.666 Da / Num. of mol.: 3 / Fragment: UNP residues 86-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC017247, FUBP1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q96AE4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 86-174 OF THE TARGET SEQUENCE - ISOFORM 2 OF FUSE-BINDING PROTEIN 1, UNIPROT ENTRY Q96AE4-2.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20.00% Glycerol, 1.60M ammonium dihydrogen phosphate, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9796,0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97961
30.97931
ReflectionResolution: 1.8→61.384 Å / Num. obs: 24100 / % possible obs: 78.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.277 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 9.17
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.850.9231.6153574174199.4
1.85-1.90.8481.8132283628188.4
1.9-1.950.633128918614.6
1.95-2.010.5083146933877199.7
2.01-2.080.3943.758771650144.1
2.08-2.150.3214.591102497168.8
2.15-2.230.3244.8128233420196.6
2.23-2.320.2266.142081166134.8
2.32-2.430.2057.1124873230199.8
2.43-2.550.1947.4119553096199.9
2.55-2.680.1698.378152087170.8
2.68-2.850.11311.691712427187.6
2.85-3.040.093141000226071100
3.04-3.290.07916.4934124421100
3.29-3.60.06817.866031781179.5
3.6-4.020.05919.549751391168.1
4.02-4.650.04623.765731773199.7
4.65-5.690.05221.457801502199.7
5.69-8.050.05120.945551168199.9
8.05-61.3840.0329.72418634199.8

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
XSCALEJuly 4, 2012data scaling
REFMAC5.7.0032refinement
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→61.384 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.119 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.122
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. PHOSPHATE (PO4) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 7. DUE TO STRONG ICE RINGS, REFLECTIONS WERE OMITTED IN THE 3.93-3.87, 3.70-3.64, 2.29-2.23, AND 1.95-1.89 RESOLUTION SHELLS LOWERING THE OVERALL COMPLETENESS TO 79.2%. THE NOMINAL RESOLUTION OF THE RESULTING DATASET IS 1.95 A WITH 4124 OBSERVED REFLECTIONS BETWEEN 1.95-1.80 (64.8% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 1228 5.1 %RANDOM
Rwork0.1716 ---
obs0.173 24098 79.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 116.26 Å2 / Biso mean: 18.7998 Å2 / Biso min: 6.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å2-0 Å2
2---0.17 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→61.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 10 320 2055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191891
X-RAY DIFFRACTIONr_bond_other_d0.0050.021883
X-RAY DIFFRACTIONr_angle_refined_deg1.5532.0252561
X-RAY DIFFRACTIONr_angle_other_deg1.25134390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9725269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.48524.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15115355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6721521
X-RAY DIFFRACTIONr_chiral_restr0.0770.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212180
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02397
X-RAY DIFFRACTIONr_mcbond_it2.0792.078955
X-RAY DIFFRACTIONr_mcbond_other2.0742.067954
X-RAY DIFFRACTIONr_mcangle_it3.5743.8031200
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 90 -
Rwork0.245 2095 -
all-2185 -
obs--99.5 %
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)
10.21560.2624-0.17950.5324-0.00430.5540.0086-0.03060.00930.0211-0.0132-0.0159-0.04530.02540.00460.0182-0.0032-0.01350.0315-0.00240.0157-1.762-1.25311.386
20.7488-0.45690.11850.3249-0.22610.5394-0.0081-0.0467-0.0071-0.00710.04030.01220.0309-0.0414-0.03220.0126-0.00730.00770.01520.00910.0302-22.095-18.38710.305
30.7867-0.0627-0.21570.5034-0.07370.1552-0.0060.0009-0.00930.02740.0001-0.00890.02420.0280.00590.0170.008-0.00550.03960.00360.00552.154-21.987.416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A97 - 171
2X-RAY DIFFRACTION2B96 - 171
3X-RAY DIFFRACTION3C95 - 171

+
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