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- PDB-5mgs: Human receptor NKR-P1 in deglycosylated form, extracellular domain -

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Basic information

Entry
Database: PDB / ID: 5mgs
TitleHuman receptor NKR-P1 in deglycosylated form, extracellular domain
ComponentsKiller cell lectin-like receptor subfamily B member 1
KeywordsIMMUNE SYSTEM / receptor / CTL fold / natural killer cell
Function / homology
Function and homology information


regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / signaling receptor activity / carbohydrate binding / cell surface receptor signaling pathway / cell surface / plasma membrane
Similarity search - Function
Natural killer cell receptor-like, C-type lectin-like domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Killer cell lectin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSkalova, T. / Blaha, J. / Stransky, J. / Koval, T. / Hasek, J. / Yuguang, Z. / Harlos, K. / Vanek, O. / Dohnalek, J.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science Foundation15-15181S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLG14009 Czech Republic
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse.
Authors: Blaha, J. / Skalova, T. / Kalouskova, B. / Skorepa, O. / Cmunt, D. / Grobarova, V. / Pazicky, S. / Polachova, E. / Abreu, C. / Stransky, J. / Koval, T. / Duskova, J. / Zhao, Y. / Harlos, K. ...Authors: Blaha, J. / Skalova, T. / Kalouskova, B. / Skorepa, O. / Cmunt, D. / Grobarova, V. / Pazicky, S. / Polachova, E. / Abreu, C. / Stransky, J. / Koval, T. / Duskova, J. / Zhao, Y. / Harlos, K. / Hasek, J. / Dohnalek, J. / Vanek, O.
History
DepositionNov 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 8, 2023Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Killer cell lectin-like receptor subfamily B member 1
B: Killer cell lectin-like receptor subfamily B member 1
C: Killer cell lectin-like receptor subfamily B member 1
D: Killer cell lectin-like receptor subfamily B member 1
E: Killer cell lectin-like receptor subfamily B member 1
F: Killer cell lectin-like receptor subfamily B member 1
G: Killer cell lectin-like receptor subfamily B member 1
H: Killer cell lectin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,40624
Polymers136,8668
Non-polymers3,53916
Water12,286682
1
A: Killer cell lectin-like receptor subfamily B member 1
B: Killer cell lectin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1016
Polymers34,2172
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Killer cell lectin-like receptor subfamily B member 1
D: Killer cell lectin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1016
Polymers34,2172
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Killer cell lectin-like receptor subfamily B member 1
F: Killer cell lectin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1016
Polymers34,2172
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: Killer cell lectin-like receptor subfamily B member 1
H: Killer cell lectin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1016
Polymers34,2172
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.806, 68.404, 101.564
Angle α, β, γ (deg.)101.88, 100.72, 100.64
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41F
51G
61H
71B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: NAG / Beg label comp-ID: NAG / End auth comp-ID: NAG / End label comp-ID: NAG / Refine code: 1 / Auth seq-ID: 502

Dom-IDAuth asym-IDLabel asym-ID
1AJ
2CN
3ER
4FT
5GV
6HX
7BL

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.145834, 0.144283, 0.978731), (0.236262, -0.965762, 0.107167), (0.960684, 0.215609, -0.174929)-40.65919, -21.26435, 119.27874
3given(-0.905736, 0.42154, -0.044116), (-0.405179, -0.891697, -0.201758), (-0.124387, -0.164865, 0.978441)35.708, -22.71762, 45.54771
4given(0.157444, 0.054016, -0.98605), (0.195855, 0.97696, 0.08479), (0.967911, -0.206472, 0.143237)82.80126, 36.12022, 98.23808
5given(0.999565, 0.026893, -0.012108), (0.02544, -0.993898, -0.107329), (-0.01492, 0.106974, -0.99415)-18.16687, -8.33247, 226.84126
6given(-0.031395, -0.118336, 0.992477), (0.187645, 0.974613, 0.122141), (-0.981735, 0.190068, -0.008393)-92.66299, 2.35432, 156.45811
7given(-0.094895, 0.107114, -0.989708), (0.162542, -0.979185, -0.12156), (-0.982128, -0.172405, 0.075509)132.3287, 14.36202, 123.45945

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Components

#1: Protein
Killer cell lectin-like receptor subfamily B member 1 / C-type lectin domain family 5 member B / HNKR-P1a / NKR-P1A / Natural killer cell surface protein P1A


Mass: 17108.312 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Protein was deglycosylated by Endo-F1 enzyme. / Source: (gene. exp.) Homo sapiens (human) / Cell: lymphocytes, natural killer cell / Gene: KLRB1, CLEC5B, NKRP1A / Plasmid: pOPINGGTneo / Cell line (production host): HEK293S GnTI- / Organ (production host): Kidney / Production host: Homo sapiens (human) / Tissue (production host): Human embryonic kidney / References: UniProt: Q12918
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 682 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42 % / Description: rod-shaped crystal
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 20% (w/v) PEG 3350, 200 mM ammonium fluoride, 200 mM lithium chloride pH 6.2, protein concentration 12 mg/ml.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→48.68 Å / Num. obs: 87081 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 7 % / Biso Wilson estimate: 24.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4353 / CC1/2: 0.671 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T3A

3t3a


Resolution: 1.9→48.68 Å / Cor.coef. Fo:Fc: 0.97 / SU B: 2.932 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 4289 5 %Random selection
Rwork0.157 ---
obs0.157 87080 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.031 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.98 Å20.66 Å2
2---0.28 Å2-2.05 Å2
3---1.6 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8251 0 224 682 9157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0198789
X-RAY DIFFRACTIONr_bond_other_d0.0020.028169
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.96311961
X-RAY DIFFRACTIONr_angle_other_deg1.003318859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09951022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68925.083421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.342151570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3621542
X-RAY DIFFRACTIONr_chiral_restr0.110.21351
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029731
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022049
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8042.8894038
X-RAY DIFFRACTIONr_mcbond_other2.8042.8894037
X-RAY DIFFRACTIONr_mcangle_it3.9834.3145040
X-RAY DIFFRACTIONr_mcangle_other3.9834.3155041
X-RAY DIFFRACTIONr_scbond_it3.7823.3434751
X-RAY DIFFRACTIONr_scbond_other3.7823.3434752
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8434.8496909
X-RAY DIFFRACTIONr_long_range_B_refined7.76624.3410352
X-RAY DIFFRACTIONr_long_range_B_other7.70224.00210081
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 25 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A2.56
C3.44
E2.56
F1.88
G4.58
H3.9
B3.62
LS refinement shellResolution: 1.9→1.949 Å
RfactorNum. reflection% reflection
Rfree0.274 290 5 %
Rwork0.271 6332 -
obs--95.35 %

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