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- PDB-3mce: Crystal structure of the NAC domain of alpha subunit of nascent p... -

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Basic information

Entry
Database: PDB / ID: 3mce
TitleCrystal structure of the NAC domain of alpha subunit of nascent polypeptide-associated complex(NAC)
ComponentsNascent polypeptide-associated complex subunit alpha
KeywordsCHAPERONE / beta-barrel like structure / NAC / homodimer
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 / wound healing ...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 / transcription coactivator activity / translation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleus / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
IODIDE ION / Nascent polypeptide-associated complex subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.396 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_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Nascent polypeptide-associated complex subunit alpha
B: Nascent polypeptide-associated complex subunit alpha
C: Nascent polypeptide-associated complex subunit alpha
D: Nascent polypeptide-associated complex subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,83812
Polymers26,8234
Non-polymers1,0158
Water95553
1
A: Nascent polypeptide-associated complex subunit alpha
B: Nascent polypeptide-associated complex subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0467
Polymers13,4112
Non-polymers6355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-10 kcal/mol
Surface area7520 Å2
MethodPISA
2
C: Nascent polypeptide-associated complex subunit alpha
D: Nascent polypeptide-associated complex subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7925
Polymers13,4112
Non-polymers3813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-8 kcal/mol
Surface area7430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.592, 59.605, 69.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 6705.729 Da / Num. of mol.: 4 / Fragment: NAC domain (UNP RESIDUES 81-133)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Alpha NAC, HSD48, NACA / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q13765
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.1 Å3/Da / Density % sol: 41.33 % / Mosaicity: 0.763 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M potassium citrate tribasic monohydrate (pH 8.3), 20% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.396→50 Å / Num. obs: 9272 / % possible obs: 99.8 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.075 / Χ2: 1.208 / Net I/σ(I): 9.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.286 / Num. unique all: 902 / Χ2: 0.692 / % possible all: 99.8

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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: 2.396→29.901 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.754 / SU ML: 0.38 / σ(F): 0.33 / Phase error: 29.86 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.277 910 9.94 %
Rwork0.247 8241 -
obs0.25 9151 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.18 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 196.51 Å2 / Biso mean: 50.786 Å2 / Biso min: 9.05 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.396→29.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 8 53 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0311852
X-RAY DIFFRACTIONf_angle_d1.9722497
X-RAY DIFFRACTIONf_chiral_restr0.178300
X-RAY DIFFRACTIONf_plane_restr0.012308
X-RAY DIFFRACTIONf_dihedral_angle_d23.182699
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.397-2.5470.371450.3071296144196
2.547-2.7430.3641460.3071344149098
2.743-3.0190.361520.2791364151699
3.019-3.4550.3031510.2421377152899
3.455-4.3510.231500.1991371152198
4.351-29.9030.2051660.21814891655100

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