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- PDB-7kx0: Crystal structure of the CD27:CD70 co-stimulatory complex -

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Basic information

Entry
Database: PDB / ID: 7kx0
TitleCrystal structure of the CD27:CD70 co-stimulatory complex
Components
  • CD27 antigen
  • CD70 antigen
KeywordsIMMUNE SYSTEM / Complex / TNF / Costimulation / Trimer
Function / homology
Function and homology information


adaptive immune memory response involving T cells and B cells / CD27 signaling pathway / B cell mediated immunity / T cell mediated immunity / TNFs bind their physiological receptors / negative regulation of T cell apoptotic process / tumor necrosis factor receptor binding / positive regulation of T cell differentiation / positive regulation of B cell differentiation / B cell proliferation ...adaptive immune memory response involving T cells and B cells / CD27 signaling pathway / B cell mediated immunity / T cell mediated immunity / TNFs bind their physiological receptors / negative regulation of T cell apoptotic process / tumor necrosis factor receptor binding / positive regulation of T cell differentiation / positive regulation of B cell differentiation / B cell proliferation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / immunoglobulin mediated immune response / positive regulation of T cell proliferation / tumor necrosis factor-mediated signaling pathway / 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 / receptor ligand activity / external side of plasma membrane / negative regulation of apoptotic process / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
CD70 antigen / Tumour necrosis factor receptor 7 / Tumour necrosis factor receptor 7, N-terminal / : / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. / Tumour necrosis factor domain ...CD70 antigen / Tumour necrosis factor receptor 7 / Tumour necrosis factor receptor 7, N-terminal / : / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. / Tumour necrosis factor domain / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
CD27 antigen / CD70 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.69 Å
AuthorsMaben, Z. / Liu, W. / Mosyak, L. / Chaparro-Riggers, J.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural delineation and phase-dependent activation of the costimulatory CD27:CD70 complex.
Authors: Liu, W. / Maben, Z. / Wang, C. / Lindquist, K.C. / Li, M. / Rayannavar, V. / Lopez Armenta, I. / Nager, A. / Pascua, E. / Dominik, P.K. / Oyen, D. / Wang, H. / Roach, R.C. / Allan, C.M. / ...Authors: Liu, W. / Maben, Z. / Wang, C. / Lindquist, K.C. / Li, M. / Rayannavar, V. / Lopez Armenta, I. / Nager, A. / Pascua, E. / Dominik, P.K. / Oyen, D. / Wang, H. / Roach, R.C. / Allan, C.M. / Mosyak, L. / Chaparro-Riggers, J.
History
DepositionDec 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD70 antigen
B: CD70 antigen
C: CD70 antigen
D: CD27 antigen
E: CD27 antigen
F: CD27 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,51216
Polymers90,7966
Non-polymers5,71610
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Individual components were purified separately and then incubated together. These mixtures were then analyzed using analytical size exclusion chromatography. A higher ...Evidence: gel filtration, Individual components were purified separately and then incubated together. These mixtures were then analyzed using analytical size exclusion chromatography. A higher molecular-weight peak arose in mixed sampled, consistent with the formation of a stable complex.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21600 Å2
ΔGint86 kcal/mol
Surface area31670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.530, 113.630, 163.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein CD70 antigen / CD27 ligand / CD27-L / Tumor necrosis factor ligand superfamily member 7


Mass: 17482.729 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD70, CD27L, CD27LG, TNFSF7 / Cell line (production host): ExpiHEK293 / Production host: Homo sapiens (human) / References: UniProt: P32970
#2: Protein CD27 antigen / CD27L receptor / T-cell activation antigen CD27 / T14 / Tumor necrosis factor receptor superfamily member 7


Mass: 12782.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD27, TNFRSF7 / Cell line (production host): ExpiHEK293 / Production host: Homo sapiens (human) / References: UniProt: P26842

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Sugars , 5 types, 9 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 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.: 3 / Source method: obtained synthetically / 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, 146 molecules

#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.8 Å3/Da / Density % sol: 56.1 % / Description: rectangular prism
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris hydrochloride pH 8 40 % 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.69→93.31 Å / Num. obs: 18602 / % possible obs: 64.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 54.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.044 / Net I/σ(I): 12
Reflection shellResolution: 2.69→2.98 Å / Redundancy: 7 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 931 / CC1/2: 0.727 / Rpim(I) all: 0.479 / % possible all: 12.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
XSCALEdata scaling
STARANISOdata reduction
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RE9, 5TL5

2re9

5tl5


Resolution: 2.69→36.72 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.415
RfactorNum. reflection% reflectionSelection details
Rfree0.236 915 4.92 %RANDOM
Rwork0.2 ---
obs0.202 18587 64.9 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 99.1 Å2 / Biso min: 22.59 Å2
Baniso -1Baniso -2Baniso -3
1-8.0438 Å20 Å20 Å2
2---1.3631 Å20 Å2
3----6.6807 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: final / Resolution: 2.69→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 392 145 6093
Biso mean--192.23 57.44 -
Num. residues----718
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2160SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1006HARMONIC5
X-RAY DIFFRACTIONt_it6148HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion898SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6441SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6148HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg8435HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2.45
X-RAY DIFFRACTIONt_other_torsion20.17
LS refinement shellResolution: 2.69→2.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.4479 17 6.42 %
Rwork0.2512 248 -
all0.2639 265 -
obs--5.79 %
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)
14.85870.9774-0.92914.82540.16385.1163-0.0172-0.1227-0.38830.0745-0.1036-0.46180.46730.20270.12080.53580.05340.705-0.21860.07340.1259-30.7353-37.761-23.9811
24.362-0.0239-0.38266.1899-0.04453.49490.2204-0.56490.2250.7074-0.01890.0928-0.28630.2015-0.20160.5913-0.04780.7527-0.1245-0.04890.1069-37.91-16.7707-12.7248
33.3772-0.9562-0.65.7282-0.46545.93820.09690.03070.3393-0.1206-0.1124-0.5177-0.3910.39810.01540.5205-0.01490.775-0.16060.02160.2036-24.1524-16.0115-33.5534
44.9967-2.0899-0.51257.6457-2.96873.8380.1579-0.14270.00860.4310.13060.5973-0.4241-0.0748-0.28850.4387-0.12370.8155-0.2834-0.08880.2949-33.26492.9532-28.2426
51.88070.9681.24526.89551.74477.90910.13480.1622-0.1872-0.58110.0325-0.3269-0.23560.0589-0.16730.42210.15830.8108-0.22280.01810.185-22.9277-38.8689-44.3631
65.85861.8153-1.22654.49310.7094.1781-0.03780.0964-0.1733-0.0759-0.0275-0.1173-0.0267-0.00750.06530.6352-0.01140.6536-0.15520.0613-0.1623-48.1849-34.8023-6.091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A54 - 193
2X-RAY DIFFRACTION2{ B|* }B54 - 193
3X-RAY DIFFRACTION3{ C|* }C54 - 193
4X-RAY DIFFRACTION4{ D|* }D25 - 124
5X-RAY DIFFRACTION5{ E|* }E26 - 124
6X-RAY DIFFRACTION6{ F|* }F26 - 124

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