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- PDB-3mcb: Crystal structure of NAC domains of human nascent polypeptide-ass... -

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Basic information

Entry
Database: PDB / ID: 3mcb
TitleCrystal structure of NAC domains of human nascent polypeptide-associated complex (NAC)
Components
  • Nascent polypeptide-associated complex subunit alpha
  • Transcription factor BTF3
KeywordsCHAPERONE / beta-barrel like structure / NAC / heterodimer
Function / homology
Function and homology information


negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / regulation of skeletal muscle fiber development / negative regulation of striated muscle cell apoptotic process / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of skeletal muscle tissue growth / cardiac ventricle development / : / skeletal muscle tissue regeneration / heart trabecula morphogenesis ...negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / regulation of skeletal muscle fiber development / negative regulation of striated muscle cell apoptotic process / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of skeletal muscle tissue growth / cardiac ventricle development / : / skeletal muscle tissue regeneration / heart trabecula morphogenesis / wound healing / protein transport / in utero embryonic development / transcription coactivator activity / translation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Nascent polypeptide-associated complex domain / Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain ...Nascent polypeptide-associated complex domain / Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / Ubiquitin Ligase Nedd4; Chain: W; / Single Sheet / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Transcription factor BTF3 / Nascent polypeptide-associated complex subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWang, L.F. / Zhang, W.C. / Wang, L. / Zhang, X.J.C. / Li, X.M. / Rao, Z.
CitationJournal: Protein Cell / Year: 2010
Title: Crystal structures of NAC domains of human nascent polypeptide-associated complex (NAC) and its alphaNAC subunit
Authors: Wang, L.F. / Zhang, W.C. / Wang, L. / Zhang, X.J.C. / Li, X.M. / Rao, Z.
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nascent polypeptide-associated complex subunit alpha
B: Transcription factor BTF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7215
Polymers12,3402
Non-polymers3813
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-12 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.794, 59.794, 156.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Nascent polypeptide-associated complex subunit alpha / NAC-alpha / Alpha-NAC


Mass: 5995.018 Da / Num. of mol.: 1 / Fragment: NAC domain (UNP RESIDUES 79-132)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Alpha NAC, HSD48, NACA / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): strain BL21 (DE3) / References: UniProt: Q13765
#2: Protein Transcription factor BTF3 / RNA polymerase B transcription factor 3 / NAC-Beta


Mass: 6345.131 Da / Num. of mol.: 1 / Fragment: NAC domain (UNP RESIDUES 97-154)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Beta NAC (BTF3b), BTF3, NACB, OK/SW-cl.8 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P20290
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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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: 3.28 Å3/Da / Density % sol: 62.47 % / Mosaicity: 0.431 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.6
Details: 0.1M sodium citrate (pH 5.6), 0.1 M NaCl, 12% (w/v) PEG 4000, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 13682 / % possible obs: 98.8 % / Redundancy: 18.3 % / Rmerge(I) obs: 0.051 / Χ2: 0.974 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.9713.40.53312571.001194.9
1.97-2.0516.50.42913330.92199.3
2.05-2.14180.33113480.994199.9
2.14-2.2518.70.22813321.391100
2.25-2.3919.20.16213701.0611100
2.39-2.5819.90.10113670.9031100
2.58-2.8420.30.07213700.941100
2.84-3.2520.20.05513930.9681100
3.25-4.0918.70.04114240.765199.8
4.09-50180.03214880.826194.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.368 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.815 / SU ML: 0.28 / σ(F): 2.03 / Phase error: 24.3 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.247 1223 10 %
Rwork0.188 11002 -
obs0.194 12225 88.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.036 Å2 / ksol: 0.401 e/Å3
Displacement parametersBiso max: 257.4 Å2 / Biso mean: 54.537 Å2 / Biso min: 24.26 Å2
Baniso -1Baniso -2Baniso -3
1--1.641 Å20 Å20 Å2
2---1.641 Å20 Å2
3---3.282 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 3 61 928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008875
X-RAY DIFFRACTIONf_angle_d1.1351184
X-RAY DIFFRACTIONf_chiral_restr0.067147
X-RAY DIFFRACTIONf_plane_restr0.004149
X-RAY DIFFRACTIONf_dihedral_angle_d17.862321
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 (%)
1.9-1.9760.364990.29888698566
1.976-2.0660.2651220.1991099122181
2.066-2.1750.2571290.1861164129387
2.175-2.3110.3021210.2181085120680
2.311-2.490.31400.1791266140693
2.49-2.740.2331460.1651314146096
2.74-3.1360.2091510.1731360151198
3.136-3.9490.2171540.1651381153598
3.949-29.3710.2451610.1891447160894

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