[English] 日本語
Yorodumi
- PDB-5mgs: Human receptor NKR-P1 in deglycosylated form, extracellular domain -

+
Open data


ID or keywords:

Loading...

-
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 ...: / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more