[English] 日本語
Yorodumi
- PDB-5tlj: COMPLEX BETWEEN HUMAN CD27 AND FAB FRAGMENTS OF ANTIBODIES M2177 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tlj
TitleCOMPLEX BETWEEN HUMAN CD27 AND FAB FRAGMENTS OF ANTIBODIES M2177 AND M2191
Components
  • CD27 antigen
  • M2177 HEAVY CHAIN
  • M2177 LIGHT CHAIN
  • M2191 HEAVY CHAIN
  • M2191 LIGHT CHAIN
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


adaptive immune memory response involving T cells and B cells / CD27 signaling pathway / TNFs bind their physiological receptors / negative regulation of T cell apoptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of B cell differentiation / positive regulation of T cell differentiation / immunoglobulin mediated immune response / extrinsic apoptotic signaling pathway / T cell activation ...adaptive immune memory response involving T cells and B cells / CD27 signaling pathway / TNFs bind their physiological receptors / negative regulation of T cell apoptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of B cell differentiation / positive regulation of T cell differentiation / immunoglobulin mediated immune response / extrinsic apoptotic signaling pathway / T cell activation / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / transmembrane signaling receptor activity / response to ethanol / cell surface receptor signaling pathway / external side of plasma membrane / negative regulation of apoptotic process / extracellular region / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 7 / Tumour necrosis factor receptor 7, N-terminal / : / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Immunoglobulins / Immunoglobulin-like ...Tumour necrosis factor receptor 7 / Tumour necrosis factor receptor 7, N-terminal / : / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
CitationJournal: Mol. Immunol. / Year: 2017
Title: Epitope-dependent mechanisms of CD27 neutralization revealed by X-ray crystallography.
Authors: Obmolova, G. / Teplyakov, A. / Malia, T.J. / Wunderler, N. / Kwok, D. / Barone, L. / Sweet, R. / Ort, T. / Scully, M. / Gilliland, G.L.
History
DepositionOct 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: M2177 LIGHT CHAIN
B: M2177 HEAVY CHAIN
C: M2191 LIGHT CHAIN
D: M2191 HEAVY CHAIN
E: M2177 LIGHT CHAIN
F: M2177 HEAVY CHAIN
G: M2191 LIGHT CHAIN
H: M2191 HEAVY CHAIN
X: CD27 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,41910
Polymers204,9949
Non-polymers4241
Water00
1
A: M2177 LIGHT CHAIN
B: M2177 HEAVY CHAIN
C: M2191 LIGHT CHAIN
D: M2191 HEAVY CHAIN
X: CD27 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0656
Polymers108,6415
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: M2177 LIGHT CHAIN
F: M2177 HEAVY CHAIN
G: M2191 LIGHT CHAIN
H: M2191 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)96,3534
Polymers96,3534
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.080, 52.960, 143.410
Angle α, β, γ (deg.)90.00, 112.19, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE DEPOSITORS STATE THAT THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO TERNARY COMPLEXES COMPOSED OF CD27 AND TWO FABS. ONE TERNARY COMPLEX INCLUDES FAB M2177 (CHAINS A AND B), FAB M2191 (CHAINS C AND D), AND CD27 (CHAIN X). THE SECOND TERNARY COMPLEX INCLUDES FAB M2177 (CHAINS E AND F), FAB M2191 (CHAINS G AND H), BUT NO CD27, WHICH IS NOT DEFINED IN THE ELECTRON DENSITY.

-
Components

-
Antibody , 4 types, 8 molecules AEBFCGDH

#1: Antibody M2177 LIGHT CHAIN


Mass: 23712.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Homo sapiens (human)
#2: Antibody M2177 HEAVY CHAIN


Mass: 24444.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Homo sapiens (human)
#3: Antibody M2191 LIGHT CHAIN


Mass: 23825.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Homo sapiens (human)
#4: Antibody M2191 HEAVY CHAIN


Mass: 24371.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 2 molecules X

#5: Protein CD27 antigen / CD27L receptor / T-cell activation antigen CD27 / T14 / Tumor necrosis factor receptor superfamily member 7


Mass: 12287.896 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 21-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD27, TNFRSF7 / Production host: unidentified baculovirus / References: UniProt: P26842
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

-
Details

Compound detailsTHE DEPOSITORS STATE THAT THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO TERNARY COMPLEXES ...THE DEPOSITORS STATE THAT THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO TERNARY COMPLEXES COMPOSED OF CD27 AND TWO FABS. ONE TERNARY COMPLEX INCLUDES FAB M2177 (CHAINS A AND B), FAB M2191 (CHAINS C AND D), AND CD27 (CHAIN X). THE SECOND TERNARY COMPLEX INCLUDES FAB M2177 (CHAINS E AND F), FAB M2191 (CHAINS G AND H), BUT NO CD27, WHICH IS NOT DEFINED IN THE ELECTRON DENSITY.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS PH 8.5, 24% PEG 3350, 0.2 M AMMONIUM CHLORIDE
PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 30, 2011 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 25023 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 9.6
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.7 / % possible all: 85.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TL5

5tl5


Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.836 / Cor.coef. Fo:Fc free: 0.727 / SU B: 62.932 / SU ML: 0.964 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.973
RfactorNum. reflection% reflectionSelection details
Rfree0.35649 1254 5 %RANDOM
Rwork0.28313 ---
obs0.28688 23667 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å2-0 Å2-0.99 Å2
2---1.87 Å20 Å2
3---3.66 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13704 0 28 0 13732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914087
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9519153
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22651798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84124.4550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.489152215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0111550
X-RAY DIFFRACTIONr_chiral_restr0.080.22128
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110559
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.6718.2527222
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.69718.5539010
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3648.1536865
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 95 -
Rwork0.367 1543 -
obs--91 %

+
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