[English] 日本語
Yorodumi
- PDB-6rqm: A blocking anti-CTLA-4 Nanobody (KN044) complexed with CTLA-4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rqm
TitleA blocking anti-CTLA-4 Nanobody (KN044) complexed with CTLA-4
Components
  • A blocking anti-CTLA-4 nanobody (KN044)
  • Cytotoxic T-lymphocyte protein 4
KeywordsIMMUNE SYSTEM / Antibody / check-point / CTLA-4 / receptor
Function / homology
Function and homology information


protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / Co-stimulation by CD28 / Co-inhibition by CTLA4 / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway ...protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / Co-stimulation by CD28 / Co-inhibition by CTLA4 / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response / immune response / positive regulation of apoptotic process / external side of plasma membrane / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane
Similarity search - Function
Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins ...Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytotoxic T-lymphocyte protein 4
Similarity search - Component
Biological speciesCamelus bactrianus (Bactrian camel)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhang, F. / Zhou, A. / Gao, H.
CitationJournal: To Be Published
Title: A blocking anti-CTLA-4 Nanobody (KN044) complexed with CTLA-4
Authors: Gao, H. / Zhou, A.
History
DepositionMay 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: A blocking anti-CTLA-4 nanobody (KN044)
A: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)28,6902
Polymers28,6902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-8 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.770, 98.770, 110.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Antibody A blocking anti-CTLA-4 nanobody (KN044)


Mass: 15308.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag residues are missing due to weak electron density.
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Protein Cytotoxic T-lymphocyte protein 4 / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


Mass: 13381.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: missing residues due to weak electron density / Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P16410
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400,

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3→68 Å / Num. obs: 6820 / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.032 / Rrim(I) all: 0.121 / Χ2: 1.03 / Net I/σ(I): 18.8
Reflection shellResolution: 3→3.18 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 3 / Num. unique obs: 1068 / Χ2: 0.99 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JDS, 3OSK

5jds

3osk


Resolution: 3→67.73 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.887 / SU B: 62.596 / SU ML: 0.469 / Cross valid method: THROUGHOUT / ESU R Free: 0.501 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31258 340 5 %RANDOM
Rwork0.24972 ---
obs0.25272 6452 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 93.615 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å21.02 Å20 Å2
2--2.03 Å2-0 Å2
3----6.59 Å2
Refinement stepCycle: LAST / Resolution: 3→67.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 0 0 1781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0131821
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171637
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.642480
X-RAY DIFFRACTIONr_angle_other_deg1.0781.5663794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79422.65879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67815273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.884158
X-RAY DIFFRACTIONr_chiral_restr0.0320.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
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_it1.4797.853953
X-RAY DIFFRACTIONr_mcbond_other1.487.851952
X-RAY DIFFRACTIONr_mcangle_it2.68111.7721186
X-RAY DIFFRACTIONr_mcangle_other2.6811.7741187
X-RAY DIFFRACTIONr_scbond_it1.1857.894867
X-RAY DIFFRACTIONr_scbond_other1.1847.897868
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.20411.7741295
X-RAY DIFFRACTIONr_long_range_B_refined4.29988.0791858
X-RAY DIFFRACTIONr_long_range_B_other4.29888.1131859
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 25 -
Rwork0.39 451 -
obs--99.79 %
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)
14.2611.03460.68920.5576-0.02981.54930.2995-0.59450.04970.0192-0.3898-0.14710.076-0.54660.09040.1560.0121-0.00590.54020.11740.095546.7511-5.0346-11.1111
23.28570.20840.66190.67611.19412.41770.09230.1192-0.184-0.0107-0.1347-0.0474-0.12450.01110.04240.2076-0.0259-0.06910.2440.11610.086372.7993-8.0061-19.9516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 128
2X-RAY DIFFRACTION2A4 - 119

+
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