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- PDB-4o2f: A peptide complexed with HLA-B*3901 -

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Basic information

Entry
Database: PDB / ID: 4o2f
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 / cell leading edge / lipid homeostasis / TAP binding / protection from natural killer cell mediated cytotoxicity / positive regulation of interferon-alpha production / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / extrinsic apoptotic signaling pathway via death domain receptors / 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 / HFE-transferrin receptor complex / positive regulation of non-canonical NF-kappaB signal transduction / 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: 1.901 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)88,6326
Polymers88,6326
Non-polymers00
Water15,889882
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)44,3163
Polymers44,3163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-18 kcal/mol
Surface area19150 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)44,3163
Polymers44,3163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-17 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.369, 95.918, 122.930
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: 852.954 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.: 882 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M sodium formate, 20% (w/v) PEG 3350, pH 8.0, 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: 1.9→50 Å / Num. all: 68094 / Num. obs: 68094 / % possible obs: 96.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.04 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 97.4

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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: 1.901→29.604 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8701 / SU ML: 0.22 / σ(F): 0 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 3445 5.06 %RANDOM
Rwork0.1854 ---
obs0.1868 68094 92.58 %-
all-68094 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.692 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 86.9 Å2 / Biso mean: 24.6309 Å2 / Biso min: 6.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.2927 Å2-0 Å2-0 Å2
2---0.6656 Å20 Å2
3----0.6271 Å2
Refinement stepCycle: LAST / Resolution: 1.901→29.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6251 0 0 882 7133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016425
X-RAY DIFFRACTIONf_angle_d1.5028722
X-RAY DIFFRACTIONf_dihedral_angle_d14.8142373
X-RAY DIFFRACTIONf_chiral_restr0.065898
X-RAY DIFFRACTIONf_plane_restr0.0031155
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9007-1.92680.27281050.22122217232280
1.9268-1.95430.23211320.21682415254787
1.9543-1.98350.25251520.20722400255289
1.9835-2.01450.23381340.20452491262590
2.0145-2.04750.21921470.19422506265391
2.0475-2.08280.22571330.18872548268192
2.0828-2.12060.2411270.19212564269193
2.1206-2.16140.18931410.18912573271493
2.1614-2.20550.21711270.19242593272093
2.2055-2.25350.23451330.19652599273294
2.2535-2.30590.24041390.19082595273494
2.3059-2.36350.23191590.19572564272393
2.3635-2.42740.20431410.20232619276094
2.4274-2.49880.26641200.20452628274895
2.4988-2.57940.21821550.20462636279195
2.5794-2.67150.25211180.20262652277095
2.6715-2.77840.241490.21412637278695
2.7784-2.90470.26861410.20882666280795
2.9047-3.05770.22331380.19872665280395
3.0577-3.24910.22781350.18482690282595
3.2491-3.49960.17131510.17662654280595
3.4996-3.85110.20271320.15962708284095
3.8511-4.40680.17471370.15112685282294
4.4068-5.54610.15851440.14732688283294
5.5461-29.60730.21521550.19572656281189
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)
11.28010.29340.20290.61610.20070.2834-0.0177-0.15960.03630.09270.00610.00160.0539-0.0015-0.00480.1071-0.0085-0.02280.09870.01260.060721.5068-18.2164-8.7445
20.6916-0.0186-0.3720.6950.03581.46510.05640.09170.0959-0.0519-0.04450.011-0.1669-0.0144-0.00140.1157-0.00080.00020.10540.01380.130333.4145-5.0319-39.066
30.540.1765-0.03070.2426-0.06660.2626-0.1991-0.04130.0266-0.08760.0865-0.0152-0.0717-0.07070.03410.13870.0164-0.01240.1309-0.0150.100121.2097-21.0509-33.1088
40.2584-0.1128-0.12110.27120.1350.3513-0.06280.1090.0858-0.05720.1-0.10390.05320.01880.00270.133-0.02510.01650.1342-0.02370.116236.5786-22.3467-35.458
51.307-0.2288-0.81490.05660.06941.1911-0.1251-0.0629-0.31850.10210.00540.05070.2337-0.0570.08980.1341-0.002-0.00160.10070.00580.15523.3251-30.2266-31.0968
60.8182-0.0062-0.9010.25440.18121.2402-0.33730.1472-0.3762-0.0179-0.0077-0.02360.3051-0.22660.1670.2315-0.00070.01750.1729-0.07280.190631.9193-36.9146-39.6631
70.0515-0.01820.15740.0825-0.22920.91890.1745-0.1162-0.51340.1996-0.28750.11520.31170.18140.07720.1970.02420.01720.1257-0.00960.230434.2074-33.482-28.3546
80.53510.0634-0.32910.39450.08260.4190.008-0.06130.0936-0.01950.0229-0.1141-0.04620.0421-0.00420.1132-0.0093-0.010.08180.0090.086327.4499-22.2791-25.9346
90.4447-0.38240.19081.0542-0.30540.88660.1730.4387-0.121-0.41550.1708-0.06010.138-0.0733-0.14710.2936-0.04790.03550.4252-0.0380.23739.4145-29.6517-47.804
101.0221-0.6358-0.81730.45440.36920.65450.13450.42080.00670.0404-0.17990.02090.1929-0.32580.01930.0605-0.066-0.04240.1305-0.09740.158920.2065-30.1683-36.7549
110.3611-0.3344-0.3160.63740.30610.30030.0360.19240.0557-0.485-0.1295-0.055-0.3689-0.12170.03350.2872-0.0186-0.00770.208-0.0180.142230.4509-22.729-43.6202
121.3388-0.0184-0.15260.136-0.1860.70640.0140.00690.0433-0.0489-0.0187-0.05580.00190.0298-0.00060.08150.00250.01750.05160.00140.086564.3306-6.9217-55.5844
131.2226-0.29010.09780.583-0.2470.510.09860.1736-0.1793-0.2229-0.04520.0360.1296-0.022-0.01080.17840.00420.01630.1147-0.02870.123359.901-15.9486-64.6069
141.1643-0.32880.68540.4079-0.35331.12760.0839-0.2048-0.1497-0.07580.0370.05930.2889-0.1210.01790.1481-0.0102-0.00440.13310.05770.128871.963-29.1273-29.8211
150.3309-0.21440.24190.4326-0.06420.1643-0.15090.04160.08140.06970.0515-0.03120.0567-0.2274-0.03320.0719-0.0440.01450.1910.02090.0858.782-13.0737-34.6253
160.14930.31740.13270.3654-0.050.53940.03050.0348-0.13940.03340.0223-0.09310.01560.105-0.02910.11010.01370.00220.16170.00510.142373.3185-10.6501-29.5973
170.49910.1222-0.00320.35760.31340.6474-0.1307-0.04010.1713-0.08830.02140.0415-0.3712-0.31330.06370.14270.0487-0.02590.18760.00690.140159.848-3.3963-34.2338
180.1351-0.12460.1070.239-0.16820.1514-0.1023-0.06830.13210.05890.23490.0104-0.1688-0.0613-0.08710.2720.08160.01060.2811-0.05560.218666.20282.0847-23.2955
190.9542-0.3503-0.84020.15440.35570.86230.2468-0.08750.70510.17310.0742-0.0648-0.61790.0899-0.15980.34870.0099-0.0020.1517-0.02880.267870.45031.228-34.6258
200.64040.1210.65570.83230.190.71750.0583-0.0983-0.1894-0.01330.0062-0.2374-0.0399-0.0847-0.02370.0990.00470.01260.11260.01470.128465.5507-9.612-40.2986
210.696-0.2507-0.15640.48180.14741.04760.013-0.55390.11060.03310.0054-0.03060.0311-0.5726-0.00380.13910.07-0.01660.2747-0.02510.140161.7336-5.4143-24.8774
220.6984-0.00140.12630.64840.08430.06640.1463-0.3722-0.14250.118-0.0722-0.20960.1905-0.4388-0.02850.12210.007-0.01780.2850.02670.118366.1162-12.7769-22.4251
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 12:30)B12 - 30
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 31:41)B31 - 41
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 42:46)B42 - 46
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 47:51)B47 - 51
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 52:71)B52 - 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 1:118)D1 - 118
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 119:174)D119 - 174
14X-RAY DIFFRACTION14CHAIN D AND (RESSEQ 175:274)D175 - 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 31:41)E31 - 41
18X-RAY DIFFRACTION18CHAIN E AND (RESSEQ 42:46)E42 - 46
19X-RAY DIFFRACTION19CHAIN E AND (RESSEQ 47:51)E47 - 51
20X-RAY DIFFRACTION20CHAIN E AND (RESSEQ 52:71)E52 - 71
21X-RAY DIFFRACTION21CHAIN E AND (RESSEQ 72:90)E72 - 90
22X-RAY DIFFRACTION22CHAIN E AND (RESSEQ 91:99)E91 - 99

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