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- PDB-3gqq: Crystal structure of the human retinal protein 4 (unc-119 homolog... -

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Basic information

Entry
Database: PDB / ID: 3gqq
TitleCrystal structure of the human retinal protein 4 (unc-119 homolog A). Northeast Structural Genomics Consortium target HR3066a
ComponentsProtein unc-119 homolog A
KeywordsSPLICING / Human retinal protein 4 / unc-119 homolog A / hRG4 / U119A_HUMAN / HR3066a / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Alternative splicing / Phosphoprotein / Sensory transduction / Vision
Function / homology
Function and homology information


negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / lipoprotein transport / positive regulation of protein tyrosine kinase activity / spindle midzone / mitotic cytokinesis / phototransduction / intercellular bridge / visual perception / endocytosis ...negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / lipoprotein transport / positive regulation of protein tyrosine kinase activity / spindle midzone / mitotic cytokinesis / phototransduction / intercellular bridge / visual perception / endocytosis / spindle pole / nervous system development / chemical synaptic transmission / synapse / lipid binding / centrosome / cytosol
Similarity search - Function
: / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / Protein unc-119 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.945 Å
AuthorsVorobiev, S.M. / Chen, Y. / Seetharaman, J. / Shastry, R. / Foote, E.L. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Shastry, R. / Foote, E.L. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the human retinal protein 4 (unc-119 homolog A).
Authors: Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Shastry, R. / Foote, E.L. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Protein unc-119 homolog A
B: Protein unc-119 homolog A
C: Protein unc-119 homolog A
D: Protein unc-119 homolog A
E: Protein unc-119 homolog A
F: Protein unc-119 homolog A


Theoretical massNumber of molelcules
Total (without water)139,76236
Polymers139,7626
Non-polymers030
Water14,466803
1
A: Protein unc-119 homolog A


Theoretical massNumber of molelcules
Total (without water)23,2947
Polymers23,2941
Non-polymers06
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein unc-119 homolog A


Theoretical massNumber of molelcules
Total (without water)23,2945
Polymers23,2941
Non-polymers04
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein unc-119 homolog A


Theoretical massNumber of molelcules
Total (without water)23,2945
Polymers23,2941
Non-polymers04
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein unc-119 homolog A


Theoretical massNumber of molelcules
Total (without water)23,2947
Polymers23,2941
Non-polymers06
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Protein unc-119 homolog A


Theoretical massNumber of molelcules
Total (without water)23,2947
Polymers23,2941
Non-polymers06
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Protein unc-119 homolog A


Theoretical massNumber of molelcules
Total (without water)23,2945
Polymers23,2941
Non-polymers04
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.888, 79.560, 189.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer according to aggregation screening

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Components

#1: Protein
Protein unc-119 homolog A / Retinal protein 4 / hRG4


Mass: 23293.604 Da / Num. of mol.: 6 / Fragment: UNP residues 56-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RG4, UNC119 / Plasmid: pET14-15C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q13432
#2: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 30 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 803 / 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: 2.1 Å3/Da / Density % sol: 41.51 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 5
Details: 40% PEG 4000, 0.1M K acetate, 0.1M Na acetate, pH 5.0, MICROBATCH UNDER OIL, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.945→50 Å / Num. all: 166290 / Num. obs: 166290 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 26.4
Reflection shellResolution: 1.945→2.02 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.87 / Num. unique all: 16637 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXD/Emodel building
RESOLVEmodel building
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXD/Ephasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.945→40.51 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. An unknown ligand bound to each hRG4 molecules has been refined. The unknown ligand (UNL) has been modeled in electron density by water molecules.
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 8332 5.03 %random
Rwork0.1912 ---
obs0.1924 165606 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.318 Å2 / ksol: 0.343 e/Å3
Refinement stepCycle: LAST / Resolution: 1.945→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8457 0 30 803 9290
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.262
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_dihedral_angle_d19.408
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.945-1.96720.25122590.2469477591
1.9672-1.99030.24872960.2335527999
1.9903-2.01460.25752970.2159515799
2.0146-2.04010.23032960.2198526299
2.0401-2.06690.24932930.2086514399
2.0669-2.09520.24142610.2075534299
2.0952-2.12520.21472780.2034518399
2.1252-2.15690.23812930.20235342100
2.1569-2.19060.23772910.20125200100
2.1906-2.22650.24892480.19155365100
2.2265-2.26490.20532580.19855284100
2.2649-2.30610.22662650.2085279100
2.3061-2.35040.23253020.20335237100
2.3504-2.39840.21142720.19645292100
2.3984-2.45050.24592740.20155275100
2.4505-2.50750.21392990.19865285100
2.5075-2.57020.22163020.20115297100
2.5702-2.63970.21022620.19465295100
2.6397-2.71740.21632420.19295326100
2.7174-2.80510.28072570.20445323100
2.8051-2.90530.23862730.21235282100
2.9053-3.02160.24592770.20825312100
3.0216-3.1590.22012760.19715284100
3.159-3.32550.20432910.1855275100
3.3255-3.53380.18492980.17255272100
3.5338-3.80640.17733040.16745257100
3.8064-4.18910.14932840.15195265100
4.1891-4.79450.17252430.1405528499
4.7945-6.03730.19562670.1719516898
6.0373-40.51830.22842740.2206493493
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)
10.827-0.55240.18750.7682-0.12850.5640.03060.0808-0.03930.0024-0.00710.02950.04150.047600.11560.0078-0.02260.1246-0.01280.146142.392861.178173.7008
20.7705-0.00550.20520.22180.00221.4014-0.02770.0652-0.03330.02030.0476-0.0245-0.082-0.141900.10740.0361-0.00960.17160.01960.12765.388773.318354.0617
30.41850.09980.07480.9242-0.24350.9146-0.02240.0443-0.01110.06280.0240.074-0.21910.0622-00.1907-0.0193-0.00640.11110.02590.13947.421494.261185.2061
40.29410.3391-0.06380.5468-0.17360.89970.0270.00980.0451-0.05420.00320.07450.0757-0.0398-00.0862-0.0104-0.01940.08950.02220.121746.356854.7584104.2313
50.25920.0261-0.21950.9777-0.36381.63770.036-0.0769-0.0391-0.01830.02240.1374-0.18270.0375-00.18260.00330.0190.09710.01080.154240.066187.4056116.5918
60.55930.22880.25570.50750.06371.34180.0205-0.0184-0.05660.06120.0537-0.08120.243-0.23450.00240.1699-0.0693-0.01720.26890.04610.124742.362398.828653.2736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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