[English] 日本語
Yorodumi
- PDB-4kzd: Crystal structure of an RNA aptamer in complex with fluorophore a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kzd
TitleCrystal structure of an RNA aptamer in complex with fluorophore and Fab
Components
  • (BL3-6 Fab antibody, ...) x 2
  • RNA (84-MER)
Keywordsimmune system/rna / G-quadruplex / Fluorescence / Fluorophore binding / In vitro / immune system-rna complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / sucrose / Chem-1TU / : / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.186 Å
AuthorsHuang, H. / Suslov, N.B. / Li, N. / Koldobskaya, Y. / Rice, P.A. / Piccirilli, J.A.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
Authors: Huang, H. / Suslov, N.B. / Li, N.S. / Shelke, S.A. / Evans, M.E. / Koldobskaya, Y. / Rice, P.A. / Piccirilli, J.A.
History
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3May 20, 2015Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: BL3-6 Fab antibody, heavy chain
L: BL3-6 Fab antibody, light chain
R: RNA (84-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0877
Polymers75,4273
Non-polymers6604
Water8,395466
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: BL3-6 Fab antibody, heavy chain
L: BL3-6 Fab antibody, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4033
Polymers48,0602
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-59 kcal/mol
Surface area19840 Å2
MethodPISA
3
R: RNA (84-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6844
Polymers27,3661
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
R: RNA (84-MER)
hetero molecules

H: BL3-6 Fab antibody, heavy chain
L: BL3-6 Fab antibody, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0877
Polymers75,4273
Non-polymers6604
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area7610 Å2
ΔGint-111 kcal/mol
Surface area33150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.425, 79.602, 95.210
Angle α, β, γ (deg.)90.00, 111.65, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Antibody , 2 types, 2 molecules HL

#1: Antibody BL3-6 Fab antibody, heavy chain


Mass: 24665.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody BL3-6 Fab antibody, light chain


Mass: 23394.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

-
RNA chain / Sugars , 2 types, 2 molecules R

#3: RNA chain RNA (84-MER)


Mass: 27366.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Spinach RNA aptamer
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 469 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-1TU / 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol


Mass: 254.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12F2N2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8% Tacsimate, 20% PEG 3,350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.19→46.69 Å / Num. all: 52772 / Num. obs: 52477 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 2.19→2.3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
RAPDmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
RAPDdata scaling
RAPDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IVK

3ivk


Resolution: 2.186→46.687 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 2000 3.81 %
Rwork0.179 --
obs0.1803 52457 98.01 %
all-52772 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.186→46.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 1815 43 466 5645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075483
X-RAY DIFFRACTIONf_angle_d1.1687864
X-RAY DIFFRACTIONf_dihedral_angle_d13.1232236
X-RAY DIFFRACTIONf_chiral_restr0.068946
X-RAY DIFFRACTIONf_plane_restr0.006675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1857-2.24040.3521420.28343589X-RAY DIFFRACTION99
2.2404-2.3010.29121410.26623573X-RAY DIFFRACTION98
2.301-2.36870.28711440.23993595X-RAY DIFFRACTION98
2.3687-2.44510.2771430.22443614X-RAY DIFFRACTION99
2.4451-2.53250.25021430.21233611X-RAY DIFFRACTION99
2.5325-2.63390.25191440.20433655X-RAY DIFFRACTION99
2.6339-2.75370.24091440.20453614X-RAY DIFFRACTION98
2.7537-2.89890.24131420.20353594X-RAY DIFFRACTION98
2.8989-3.08050.23461430.19313601X-RAY DIFFRACTION99
3.0805-3.31830.22841430.18173584X-RAY DIFFRACTION98
3.3183-3.65210.23091410.16543566X-RAY DIFFRACTION96
3.6521-4.18030.17341420.15213597X-RAY DIFFRACTION98
4.1803-5.26560.15181430.13733608X-RAY DIFFRACTION97
5.2656-46.69780.18061450.16963656X-RAY DIFFRACTION97

+
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