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- PDB-4lcy: Crystal structure of HLA-b46 at 1.6 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 4lcy
TitleCrystal structure of HLA-b46 at 1.6 angstrom resolution
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-46 alpha chain
  • dengue1 poly peptide
KeywordsMEMBRANE PROTEIN / antigen presenting / cell surface / HLA-B46
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / flavivirin / protection from natural killer cell mediated cytotoxicity / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / flavivirin / protection from natural killer cell mediated cytotoxicity / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / detection of bacterium / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / 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 / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / 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 / peptide antigen 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 / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / viral capsid / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / double-stranded RNA binding / nucleoside-triphosphate phosphatase / negative regulation of neuron projection development / protein-folding chaperone binding / channel activity / ER-Phagosome pathway / protein refolding / early endosome membrane / monoatomic ion transmembrane transport / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / adaptive immune response / amyloid fibril formation / methyltransferase cap1 activity / intracellular iron ion homeostasis / learning or memory / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / immune response / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / symbiont-mediated activation of host autophagy / lysosomal membrane / innate immune response / external side of plasma membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / DEAD box, Flavivirus / Flavivirus DEAD domain / 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 / 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 E-set / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Genome polyprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Dengue virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, J.X.
CitationJournal: To be Published
Title: Crystal Structure Analysis of the Human Leukocyte Antigen B*46:01
Authors: Liu, J.X.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 20, 2024Group: Structure summary / Category: 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: HLA class I histocompatibility antigen, B-46 alpha chain
B: Beta-2-microglobulin
C: dengue1 poly peptide
F: HLA class I histocompatibility antigen, B-46 alpha chain
H: Beta-2-microglobulin
J: dengue1 poly peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,59812
Polymers89,4606
Non-polymers1386
Water20,6451146
1
A: HLA class I histocompatibility antigen, B-46 alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8323
Polymers31,7861
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9022
Polymers11,8791
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: dengue1 poly peptide


Theoretical massNumber of molelcules
Total (without water)1,0641
Polymers1,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: HLA class I histocompatibility antigen, B-46 alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8323
Polymers31,7861
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9022
Polymers11,8791
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
J: dengue1 poly peptide


Theoretical massNumber of molelcules
Total (without water)1,0641
Polymers1,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: HLA class I histocompatibility antigen, B-46 alpha chain
B: Beta-2-microglobulin
C: dengue1 poly peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7996
Polymers44,7303
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-52 kcal/mol
Surface area19080 Å2
MethodPISA
8
F: HLA class I histocompatibility antigen, B-46 alpha chain
H: Beta-2-microglobulin
J: dengue1 poly peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7996
Polymers44,7303
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-52 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.950, 89.730, 94.620
Angle α, β, γ (deg.)90.00, 98.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, B-46 alpha chain / Bw-46 / MHC class I antigen B*46


Mass: 31786.107 Da / Num. of mol.: 2 / Fragment: UNP residues 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: B46:01 / Gene: HLA, HLA-B, HLAB / Plasmid: pET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P30484, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, BETA 2 MICROGLOBULIN, CDABP0092, HDCMA22P / Plasmid: pET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide dengue1 poly peptide


Mass: 1064.321 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence is one fragment of Dengue Virus 1 polyprotein.
Source: (synth.) Dengue virus 1 / References: UniProt: P17763*PLUS
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1146 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF ENTITY 3 HAS IEDB ID 124151.

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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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M BIS-TRIS pH 5.5, 25% POLYETHYLENE GLYCOL 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→25.2 Å / Num. all: 108570 / Num. obs: 107515 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.049 / Rsym value: 0.041 / Net I/σ(I): 12.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 5.7 / Num. unique all: 15693 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C9N

3c9n


Resolution: 1.6→25.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.309 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.019 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20111 5346 5 %RANDOM
Rwork0.17243 ---
obs0.17383 102144 98.92 %-
all-108570 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.109 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6305 0 6 1146 7457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196485
X-RAY DIFFRACTIONr_bond_other_d0.0010.025878
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9348804
X-RAY DIFFRACTIONr_angle_other_deg0.8143.00213492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2065760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50123.011352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.588151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4771566
X-RAY DIFFRACTIONr_chiral_restr0.0970.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021630
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 391 -
Rwork0.207 7522 -
obs--99.26 %

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