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- PDB-5tl5: COMPLEX BETWEEN HUMAN CD27 AND ANTIBODY M2177 -

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Basic information

Entry
Database: PDB / ID: 5tl5
TitleCOMPLEX BETWEEN HUMAN CD27 AND ANTIBODY M2177
Components
  • CD27 antigen
  • 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: 1.8 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of CD27 in complex with a neutralizing noncompeting antibody.
Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Gilliland, G.L.
History
DepositionOct 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / entity_poly / 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 / _diffrn_radiation_wavelength.wavelength / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
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

Downloads & links

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Assembly

Deposited unit
L: M2177 LIGHT CHAIN
H: M2177 HEAVY CHAIN
A: CD27 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7625
Polymers60,4443
Non-polymers3172
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-39 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)274.200, 37.410, 61.080
Angle α, β, γ (deg.)90.00, 98.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody M2177 LIGHT CHAIN


Mass: 23712.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody M2177 HEAVY CHAIN


Mass: 24444.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules A

#3: 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
#5: 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.: 1
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

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Non-polymers , 2 types, 306 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.58 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES PH 6.5, 17% PEG 4000, 0.2 M AMMONIUM CITRATE
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 56791 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 4.1 / % possible all: 96.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
REFMAC5.5.0109refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IQW

1iqw


Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.761 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.119
RfactorNum. reflection% reflectionSelection details
Rfree0.23178 1138 2 %RANDOM
Rwork0.1965 ---
obs0.19725 54736 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å2-1.24 Å2
2---0.34 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4069 0 19 305 4393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224214
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9555738
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1365539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90424.675169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18915666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3461515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2626
X-RAY DIFFRACTIONr_gen_planes_refined00.0213201
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_it3.01122686
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.62944331
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it12.661881528
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it16.178881405
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: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 76 -
Rwork0.276 3911 -
obs--100 %

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