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- PDB-4dwf: Crystal structure of a HLA-B associated transcript 3 (BAT3) from ... -

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Basic information

Entry
Database: PDB / ID: 4dwf
TitleCrystal structure of a HLA-B associated transcript 3 (BAT3) from Homo sapiens at 1.80 A resolution
ComponentsHLA-B-associated transcript 3
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ubiquitin-like domain / BAT3 protein / PF00240 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / : / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / synaptonemal complex assembly / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding ...BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / : / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / synaptonemal complex assembly / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding / natural killer cell activation / endoplasmic reticulum stress-induced pre-emptive quality control / ERAD pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / proteasome binding / ubiquitin-specific protease binding / : / regulation of embryonic development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / polyubiquitin modification-dependent protein binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Hsp70 protein binding / kidney development / proteasomal protein catabolic process / negative regulation of proteolysis / lung development / regulation of protein stability / brain development / ribosome binding / chromatin organization / ubiquitin-dependent protein catabolic process / spermatogenesis / cell differentiation / protein stabilization / signaling receptor binding / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues ...Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Large proline-rich protein BAG6
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 (TCELL)
CitationJournal: To be published
Title: Crystal structure of a HLA-B associated transcript 3 (BAT3) from Homo sapiens at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-B-associated transcript 3
B: HLA-B-associated transcript 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3006
Polymers19,9162
Non-polymers3844
Water3,063170
1
A: HLA-B-associated transcript 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1503
Polymers9,9581
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HLA-B-associated transcript 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1503
Polymers9,9581
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.320, 74.090, 43.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein HLA-B-associated transcript 3 / Large proline-rich protein BAG6 / BAG family molecular chaperone regulator 6 / BCL2-associated ...Large proline-rich protein BAG6 / BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG-6 / BAG6 / Protein G3 / Protein Scythe


Mass: 9958.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG6, BAT3, BC003133, G3 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: P46379
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 13-101 OF THE TARGET SEQUENCE. SEQUENCE NUMBERING IS BASED ON ISOFORM 1 OF UNIPROT-KB ID P46379.

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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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2.0M (NH4)2SO4, 0.2M K/Na Tartrate, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97949, 0.97903
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 1, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979491
30.979031
ReflectionResolution: 1.8→28.33 Å / Num. obs: 18720 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.113 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.860.4871.65853310093.6
1.86-1.940.3122.37111373498.6
1.94-2.030.2123.46810355898.9
2.03-2.130.1714.46268325798.9
2.13-2.270.1235.97100368798.6
2.27-2.440.0887.96471336098.7
2.44-2.690.0610.86828353998.4
2.69-3.070.03716.56595341998.5
3.07-3.870.02423.66793349998
3.870.01930.76770343896.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→28.33 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.014 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS 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. SULFATE IONS (SO4) FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 964 5.2 %RANDOM
Rwork0.1825 ---
obs0.1854 18696 99.24 %-
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: 99 Å2 / Biso mean: 37.9515 Å2 / Biso min: 21.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--2.44 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 20 170 1438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021320
X-RAY DIFFRACTIONr_bond_other_d0.0010.02909
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9921793
X-RAY DIFFRACTIONr_angle_other_deg1.00532249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9595170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.11325.48462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2115253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.659158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02231
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 55 -
Rwork0.305 1155 -
all-1210 -
obs--98.13 %
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)
10.8103-0.0650.29192.1617-0.03943.97490.02130.1102-0.10040.08150.119-0.01960.24520.1366-0.14030.06770.0164-0.00330.0252-0.01870.08218.83613.17527.791
21.8177-0.19290.45742.32160.13783.48060.01670.10270.13540.09370.03140.0016-0.16830.0812-0.04810.0618-0.0060.00120.01080.01950.068815.48123.9396.273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 90
2X-RAY DIFFRACTION2B0 - 90

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