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- PDB-5e08: Specific Recognition of a Single-stranded RNA Sequence by an Engi... -

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Basic information

Entry
Database: PDB / ID: 500000000
TitleSpecific Recognition of a Single-stranded RNA Sequence by an Engineered Synthetic Antibody Fragment
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • RNA
KeywordsImmune system/RNA / antibody / Fab / ssRNA / Immune system-RNA complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsHuang, H. / Qin, D. / Li, N. / Shao, Y. / Staley, J.P. / Kossiakoff, A.A. / Koide, S. / Piccirilli, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081987 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088656 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102489 United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment.
Authors: Shao, Y. / Huang, H. / Qin, D. / Li, N.S. / Koide, A. / Staley, J.P. / Koide, S. / Kossiakoff, A.A. / Piccirilli, J.A.
History
DepositionSep 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab Heavy Chain
L: Fab Light Chain
N: RNA


Theoretical massNumber of molelcules
Total (without water)52,2573
Polymers52,2573
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-39 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.515, 63.401, 57.061
Angle α, β, γ (deg.)90.00, 97.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-318-

HOH

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Components

#1: Antibody Fab Heavy Chain


Mass: 24959.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab Light Chain


Mass: 23444.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: RNA chain RNA


Mass: 3852.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.8 M Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.38→60.4 Å / Num. obs: 28135 / % possible obs: 98.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
PHENIXdev_1405refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IVK

3ivk


Resolution: 2.38→60.4 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1793 7.1 %Random selection
Rwork0.2094 ---
obs0.2112 28135 98.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→60.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 255 0 76 3710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063759
X-RAY DIFFRACTIONf_angle_d1.4275162
X-RAY DIFFRACTIONf_dihedral_angle_d16.4041372
X-RAY DIFFRACTIONf_chiral_restr0.112583
X-RAY DIFFRACTIONf_plane_restr0.006612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.43950.42431380.38371797X-RAY DIFFRACTION95
2.4395-2.50550.37051410.34971841X-RAY DIFFRACTION98
2.5055-2.57920.37021410.32681851X-RAY DIFFRACTION99
2.5792-2.66240.31511440.30641875X-RAY DIFFRACTION99
2.6624-2.75760.29271410.28991851X-RAY DIFFRACTION98
2.7576-2.8680.30781400.26341830X-RAY DIFFRACTION98
2.868-2.99850.34121440.25971881X-RAY DIFFRACTION99
2.9985-3.15660.28541450.23131896X-RAY DIFFRACTION100
3.1566-3.35440.24621430.21711862X-RAY DIFFRACTION99
3.3544-3.61330.19351380.18721841X-RAY DIFFRACTION97
3.6133-3.97690.21341430.17731872X-RAY DIFFRACTION99
3.9769-4.55220.16041460.15181907X-RAY DIFFRACTION100
4.5522-5.73460.17271440.16151892X-RAY DIFFRACTION98
5.7346-60.39480.20651490.191942X-RAY DIFFRACTION99

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