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- PDB-4o2e: A peptide complexed with HLA-B*3901 -

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Basic information

Entry
Database: PDB / ID: 4o2e
TitleA peptide complexed with HLA-B*3901
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-39 alpha chain
  • Peptide from ATP-dependent RNA helicase DDX3X
KeywordsIMMUNE SYSTEM / Ig-like
Function / homology
Function and homology information


CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation / gamete generation ...CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation / gamete generation / positive regulation of protein K63-linked ubiquitination / NLRP3 inflammasome complex / cellular response to arsenic-containing substance / poly(A) binding / regulation of interleukin-12 production / regulation of dendritic cell differentiation / gamma-tubulin binding / regulation of T cell anergy / P granule / cellular response to osmotic stress / regulation of interleukin-6 production / negative regulation of non-canonical NF-kappaB signal transduction / cytoplasmic pattern recognition receptor signaling pathway / transcription factor binding / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of intrinsic apoptotic signaling pathway / lipid homeostasis / cell leading edge / TAP binding / positive regulation of interferon-alpha production / protection from natural killer cell mediated cytotoxicity / positive regulation of translational initiation / ribosomal small subunit binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / extrinsic apoptotic signaling pathway via death domain receptors / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of type I interferon production / positive regulation of G1/S transition of mitotic cell cycle / detection of bacterium / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / translation initiation factor binding / signaling adaptor activity / stress granule assembly / intrinsic apoptotic signaling pathway / DNA helicase activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / positive regulation of translation / DAP12 interactions / protein serine/threonine kinase activator activity / transferrin transport / cytosolic ribosome assembly / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / chromosome segregation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / translational initiation / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / positive regulation of non-canonical NF-kappaB signal transduction / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / negative regulation of cell growth / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / cellular response to virus / peptide antigen binding / mRNA 5'-UTR binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / response to virus / RNA stem-loop binding / specific granule lumen / Wnt signaling pathway / phagocytic vesicle membrane / recycling endosome membrane
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Helicase conserved C-terminal domain / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / helicase superfamily c-terminal domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DDX3X / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å
AuthorsSun, M. / Liu, J. / Qi, J. / Tefsen, B. / Shi, Y. / Yan, J. / Gao, G.F.
CitationJournal: J.Immunol. / Year: 2014
Title: N alpha-terminal acetylation for T cell recognition: molecular basis of MHC class I-restricted n alpha-acetylpeptide presentation
Authors: Sun, M. / Liu, J. / Qi, J. / Tefsen, B. / Shi, Y. / Yan, J. / Gao, G.F.
History
DepositionDec 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-39 alpha chain
B: Beta-2-microglobulin
C: Peptide from ATP-dependent RNA helicase DDX3X
D: HLA class I histocompatibility antigen, B-39 alpha chain
E: Beta-2-microglobulin
F: Peptide from ATP-dependent RNA helicase DDX3X


Theoretical massNumber of molelcules
Total (without water)88,8066
Polymers88,8066
Non-polymers00
Water14,178787
1
A: HLA class I histocompatibility antigen, B-39 alpha chain
B: Beta-2-microglobulin
C: Peptide from ATP-dependent RNA helicase DDX3X


Theoretical massNumber of molelcules
Total (without water)44,4033
Polymers44,4033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-16 kcal/mol
Surface area19070 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, B-39 alpha chain
E: Beta-2-microglobulin
F: Peptide from ATP-dependent RNA helicase DDX3X


Theoretical massNumber of molelcules
Total (without water)44,4033
Polymers44,4033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-17 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.939, 103.967, 122.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, B-39 alpha chain / MHC class I antigen B*39


Mass: 31714.873 Da / Num. of mol.: 2 / Fragment: UNP residues 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P30475, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Peptide from ATP-dependent RNA helicase DDX3X / DEAD box protein 3 / X-chromosomal / DEAD box / X isoform / Helicase-like protein 2 / HLP2


Mass: 940.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O00571
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / 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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M ammonium acetate, 0.1M Bis-Tris (pH 6.5), 20% (w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 66979 / Num. obs: 66979 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.06 Å2
Reflection shellResolution: 1.98→2.07 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BST

2bst


Resolution: 1.981→23.924 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8646 / SU ML: 0.24 / σ(F): 0 / Phase error: 20.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 3388 5.06 %
Rwork0.1856 --
obs0.1868 66979 93.67 %
all-66979 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.532 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 110.74 Å2 / Biso mean: 31.4079 Å2 / Biso min: 8.54 Å2
Baniso -1Baniso -2Baniso -3
1--1.1365 Å20 Å2-0 Å2
2--1.5397 Å20 Å2
3----0.4032 Å2
Refinement stepCycle: LAST / Resolution: 1.981→23.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6263 0 0 787 7050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096436
X-RAY DIFFRACTIONf_angle_d0.8758736
X-RAY DIFFRACTIONf_dihedral_angle_d14.1772376
X-RAY DIFFRACTIONf_chiral_restr0.075900
X-RAY DIFFRACTIONf_plane_restr0.0031156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9809-2.00920.2295820.21391859194166
2.0092-2.03920.25251300.21782495262589
2.0392-2.0710.21171350.20352452258789
2.071-2.1050.22541450.20672518266390
2.105-2.14120.28981430.19432519266291
2.1412-2.18020.24561460.20062512265890
2.1802-2.22210.20181150.19782605272091
2.2221-2.26740.24781290.19762585271493
2.2674-2.31660.22711430.19592555269892
2.3166-2.37050.20751460.20742574272092
2.3705-2.42970.21481290.20292624275392
2.4297-2.49530.23451450.20062606275193
2.4953-2.56870.26471320.20482671280395
2.5687-2.65150.25361320.2082701283395
2.6515-2.74610.21821600.20432689284996
2.7461-2.85590.24271620.20492743290597
2.8559-2.98570.20851290.20622827295699
2.9857-3.14270.21261320.19462814294699
3.1427-3.33920.22741620.189928242986100
3.3392-3.59620.21021330.185328602993100
3.5962-3.95660.18211700.160328443014100
3.9566-4.52580.15451490.146228833032100
4.5258-5.68930.16331710.147928883059100
5.6893-23.9260.20511680.19582943311197
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)
10.73310.02370.21860.7273-0.06390.3302-0.0318-0.10860.00020.03480.0654-0.0297-0.0162-0.05030.00580.08440.0006-0.00520.1306-0.00520.109922.1144-20.8982-8.609
20.3885-0.0662-0.35910.4051-0.23430.6167-0.01280.21640.05680.03750.09130.0616-0.1474-0.1384-0.00850.1735-0.05110.01750.24910.04390.191834.9356-5.2444-37.5154
30.1728-0.12730.09740.3155-0.22340.174-0.04850.05150.0005-0.25310.16020.0746-0.1555-0.1187-0.03220.2544-0.12510.07560.3367-0.04830.161122.1717-21.6927-33.1496
40.0422-0.0172-0.01490.01520.04730.171-0.0778-0.056-0.0422-0.10030.0719-0.13210.03460.0608-0.02510.1916-0.16650.4460.6496-0.34110.374545.118-21.4895-39.4914
50.33930.0755-0.16560.2391-0.21690.258-0.04920.1096-0.0199-0.18690.1974-0.11690.07770.11010.03130.2322-0.0810.08180.2787-0.09380.212332.0363-23.8113-32.6521
60.0896-0.17440.19210.4725-0.02260.9442-0.0410.1223-0.1667-0.21650.2274-0.18430.1231-0.06240.19220.3587-0.12880.10450.2171-0.11490.221427.0373-32.9318-34.8124
70.18070.02720.0640.136-0.04390.1247-0.0119-0.053-0.0881-0.2170.1037-0.22240.22880.0267-0.04940.2727-0.00970.00730.1377-0.03360.233131.153-29.5586-25.1757
80.3271-0.0202-0.20850.1239-0.18210.6046-0.03010.12840.0911-0.16440.2791-0.11720.0297-0.04990.0330.1943-0.06540.04490.1503-0.06340.175628.8284-23.4417-27.5953
90.10780.0298-0.01780.0441-0.02310.01280.02230.06850.0202-0.04630.0786-0.04430.0341-0.0120.03090.6472-0.24650.31090.7743-0.18040.616740.3949-28.5433-48.6128
100.07990.07320.01630.18810.05940.1635-0.03980.133-0.1138-0.0820.1307-0.20550.060800.07280.3195-0.15380.0390.3152-0.0910.198521.1586-30.4616-37.6064
110.0655-0.02520.03170.10170.0930.1415-0.08220.0351-0.0245-0.1336-0.0358-0.06850.0265-0.0542-0.10630.531-0.30450.32270.5654-0.11970.105331.2862-22.456-43.7438
121.0487-0.1703-0.08650.5364-0.11760.97750.04020.1557-0.0002-0.13610.0148-0.02180.1832-0.05740.040.1862-0.014-0.00760.10940.01250.1105-15.5561-7.7301-57.6261
130.4413-0.0280.20370.2474-0.02920.08320.0506-0.16570.0073-0.0615-0.0908-0.0190.0093-0.0105-0.01390.23190.0450.0080.26430.03510.2577-1.1757-25.2305-31.83
140.2159-0.08540.08270.1704-0.05940.29510.0982-0.1855-0.158-0.32630.04960.12030.2896-0.13590.04840.238-0.0098-0.06420.13550.07420.2389-7.3656-30.5415-30.7888
150.4348-0.12640.24060.3952-0.10540.4076-0.092-0.1048-0.0365-0.0731-0.0034-0.04920.0331-0.36520.05920.18290.0203-0.00990.24840.01180.1206-19.2779-12.8491-33.9555
160.36610.32860.13560.36940.19610.4963-0.06070.0159-0.1569-0.01620.0672-0.1851-0.10040.0095-0.0040.15370.026-0.00910.16980.02810.1693-4.5748-11.1172-29.0082
170.23520.0354-0.01020.277-0.04310.2048-0.1711-0.12860.13310.02870.1853-0.0024-0.363-0.17570.00940.26960.0799-0.04430.201-0.00860.1529-15.8324-1.8208-29.1931
180.1624-0.0688-0.10440.066-0.0320.2315-0.02510.03640.12990.0903-0.1014-0.0694-0.17930.03660.05750.33350.0407-0.01460.1377-0.01110.2527-7.2521.2734-32.9063
190.3634-0.1410.24690.1936-0.02230.37590.0122-0.089-0.18660.05420.0796-0.19270.0340.0125-0.06050.16220.0037-0.01160.12360.03110.1679-12.4572-8.9902-39.448
201.3127-0.53830.74361.0041-0.34970.5082-0.0111-0.2497-0.04210.21260.1436-0.02910.0304-0.0698-0.04350.310.0322-0.050.22390.01290.2125-3.9812-7.7145-14.8768
210.27930.12220.06150.30330.02290.02880.0107-0.26950.04420.14730.0023-0.0369-0.0881-0.4394-0.01790.19370.07220.00860.33580.03670.1377-17.2274-9.1056-25.2652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:174)A1 - 174
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 175:274)A175 - 274
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 1:11)B1 - 11
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 12:19)B12 - 19
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 20:30)B20 - 30
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 31:46)B31 - 46
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 47:56)B47 - 56
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 57:71)B57 - 71
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 72:77)B72 - 77
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 78:90)B78 - 90
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 91:99)B91 - 99
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 1:174)D1 - 174
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 175:197)D175 - 197
14X-RAY DIFFRACTION14CHAIN D AND (RESSEQ 198:274)D198 - 274
15X-RAY DIFFRACTION15CHAIN E AND (RESSEQ 1:11)E1 - 11
16X-RAY DIFFRACTION16CHAIN E AND (RESSEQ 12:30)E12 - 30
17X-RAY DIFFRACTION17CHAIN E AND (RESSEQ 31:46)E31 - 46
18X-RAY DIFFRACTION18CHAIN E AND (RESSEQ 47:51)E47 - 51
19X-RAY DIFFRACTION19CHAIN E AND (RESSEQ 52:71)E52 - 71
20X-RAY DIFFRACTION20CHAIN E AND (RESSEQ 72:77)E72 - 77
21X-RAY DIFFRACTION21CHAIN E AND (RESSEQ 78:99)E78 - 99

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