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- PDB-4ive: Crystal structure of a polyadenylate-binding protein 3 (PABPC3) f... -

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Basic information

Entry
Database: PDB / ID: 4ive
TitleCrystal structure of a polyadenylate-binding protein 3 (PABPC3) from Homo sapiens at 2.30 A resolution
ComponentsPolyadenylate-binding protein 3
KeywordsRNA BINDING PROTEIN / PABP unique domain / PF00658 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / RNA-BINDING PROTEIN / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


mRNA metabolic process / poly(A) binding / poly(U) RNA binding / mRNA 3'-UTR binding / cytoplasmic stress granule / ribonucleoprotein complex / extracellular exosome / nucleus / cytoplasm / cytosol
Similarity search - Function
c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / : / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE domain ...c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / : / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE domain / RNA recognition motif domain, eukaryote / RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polyadenylate-binding protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a polyadenylate-binding protein 3 (PABPC3) from Homo sapiens at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionJan 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 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
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyadenylate-binding protein 3
B: Polyadenylate-binding protein 3
C: Polyadenylate-binding protein 3
D: Polyadenylate-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9056
Polymers42,8354
Non-polymers712
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-40 kcal/mol
Surface area14880 Å2
MethodPISA
2
A: Polyadenylate-binding protein 3
B: Polyadenylate-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4533
Polymers21,4172
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-15 kcal/mol
Surface area8490 Å2
MethodPISA
3
C: Polyadenylate-binding protein 3
D: Polyadenylate-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4533
Polymers21,4172
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-15 kcal/mol
Surface area8470 Å2
MethodPISA
4
A: Polyadenylate-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7442
Polymers10,7091
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Polyadenylate-binding protein 3


Theoretical massNumber of molelcules
Total (without water)10,7091
Polymers10,7091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
C: Polyadenylate-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7442
Polymers10,7091
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
D: Polyadenylate-binding protein 3


Theoretical massNumber of molelcules
Total (without water)10,7091
Polymers10,7091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.395, 67.395, 101.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Polyadenylate-binding protein 3 / PABP-3 / Poly(A)-binding protein 3 / Testis-specific poly(A)-binding protein


Mass: 10708.643 Da / Num. of mol.: 4 / Fragment: PABC domain residues 535-631
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC027617, PABP3, PABPC3, PABPL3 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9H361
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (535-631) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (535-631) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.62
Details: 26.00% polyethylene glycol 6000, 0.1M MES pH 5.62, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979493,0.918401,0.979284
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794931
20.9184011
30.9792841
ReflectionResolution: 2.3→43.128 Å / Num. obs: 20106 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.537 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.03
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.3-2.380.7562.4127271919197.8
2.38-2.480.5753.41610421171100
2.48-2.590.4214.51490319601100
2.59-2.730.3046.11555720431100
2.73-2.90.2138.31526120011100
2.9-3.120.14311.91488019621100
3.12-3.430.10715.51487519961100
3.43-3.930.0919126572004198
3.93-4.930.06323.6139181987199.8
4.93-43.1280.05325151262103199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→43.128 Å / Cor.coef. Fo:Fc: 0.9279 / Cor.coef. Fo:Fc free: 0.9277 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. CHLORIDE IONS MODELED ARE PRESENT IN CRYSTALLIZATION BUFFER. 3. A MET- ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. CHLORIDE IONS MODELED ARE PRESENT IN CRYSTALLIZATION BUFFER. 3. 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. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 1016 5.07 %RANDOM
Rwork0.2005 ---
obs0.2011 20056 99.58 %-
Displacement parametersBiso max: 165.61 Å2 / Biso mean: 56.6623 Å2 / Biso min: 19.82 Å2
Baniso -1Baniso -2Baniso -3
1--5.0464 Å20 Å20 Å2
2---5.0464 Å20 Å2
3---10.0927 Å2
Refine analyzeLuzzati coordinate error obs: 0.357 Å
Refinement stepCycle: LAST / Resolution: 2.3→43.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 2 133 2445
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1208SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes63HARMONIC2
X-RAY DIFFRACTIONt_gen_planes354HARMONIC5
X-RAY DIFFRACTIONt_it2422HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion334SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2964SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2422HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3292HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion2.67
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2442 132 4.58 %
Rwork0.1995 2747 -
all0.2015 2879 -
obs--99.58 %
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)
15.2051-0.5073-2.91042.74631.70778.3043-0.11950.479-0.02450.01760.09140.2472-0.023-0.44410.0281-0.17220.04110.0436-0.00790.0104-0.157132.59615.206734.9959
24.5334-0.1746-1.31912.0931.3948.31550.16010.54420.2683-0.248-0.38090.2485-0.47-0.54420.2208-0.25940.152-0.04710.1354-0.0262-0.158114.033610.103340.7462
34.8886-2.65-0.62397.5299-0.03124.265-0.0234-0.0686-0.54420.5297-0.13050.4828-0.1313-0.23670.154-0.13530.02070.0392-0.1298-0.0395-0.118712.409414.540967.0452
41.7851-0.84290.16312.7042-1.73188.3155-0.0432-0.0238-0.0661-0.0481-0.3216-0.26960.25650.51480.3648-0.16140.03130.0315-0.01360.0475-0.062427.61012.77461.1619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|537 - 612}A537 - 612
2X-RAY DIFFRACTION2{B|538 - 614}B538 - 614
3X-RAY DIFFRACTION3{C|538 - 613}C538 - 613
4X-RAY DIFFRACTION4{D|538 - 613}D538 - 613

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