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- PDB-5tlk: COMPLEX BETWEEN HUMAN CD27 AND FAB FRAGMENTS OF ANTIBODIES M2177 ... -

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Basic information

Entry
Database: PDB / ID: 5tlk
TitleCOMPLEX BETWEEN HUMAN CD27 AND FAB FRAGMENTS OF ANTIBODIES M2177 AND H2191
Components
  • CD27 antigen
  • H2191 HEAVY CHAIN
  • H2191 LIGHT CHAIN
  • M2177 HEAVY CHAIN
  • M2177 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 T cell differentiation / positive regulation of B 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 T cell differentiation / positive regulation of B 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / diffrn_radiation_wavelength / 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 / _diffrn_radiation_wavelength.wavelength / _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.ptnr1_label_asym_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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M2177 LIGHT CHAIN
B: M2177 HEAVY CHAIN
C: H2191 LIGHT CHAIN
D: H2191 HEAVY CHAIN
E: M2177 LIGHT CHAIN
F: M2177 HEAVY CHAIN
G: H2191 LIGHT CHAIN
H: H2191 HEAVY CHAIN
X: CD27 antigen
Y: CD27 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,11712
Polymers217,26810
Non-polymers8492
Water1,35175
1
A: M2177 LIGHT CHAIN
B: M2177 HEAVY CHAIN
C: H2191 LIGHT CHAIN
D: H2191 HEAVY CHAIN
X: CD27 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0586
Polymers108,6345
Non-polymers4241
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: M2177 LIGHT CHAIN
F: M2177 HEAVY CHAIN
G: H2191 LIGHT CHAIN
H: H2191 HEAVY CHAIN
Y: CD27 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0586
Polymers108,6345
Non-polymers4241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.710, 52.960, 140.600
Angle α, β, γ (deg.)90.00, 109.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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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 H2191 LIGHT CHAIN


Mass: 24072.822 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 H2191 HEAVY CHAIN


Mass: 24116.967 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)

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Protein / Sugars / Non-polymers , 3 types, 79 molecules XY

#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.: 2 / 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.: 2
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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS PH 8.5, 22% PEG 3350 / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 53961 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.6 / % possible all: 88.3

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Processing

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

5tl5


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.543 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374
RfactorNum. reflection% reflectionSelection details
Rfree0.26318 1105 2.1 %RANDOM
Rwork0.21318 ---
obs0.21422 52594 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.54 Å2-0 Å2-0.26 Å2
2---0.29 Å20 Å2
3----2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14156 0 56 75 14287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01914590
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.251.95619848
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91651842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37724.296582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.478152306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.551558
X-RAY DIFFRACTIONr_chiral_restr0.0770.22190
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111032
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_it2.9177.9837416
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.80417.9459242
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5768.2447174
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.46620207
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: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 86 -
Rwork0.298 3782 -
obs--99.2 %

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