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- PDB-4h5s: Complex structure of Necl-2 and CRTAM -

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Basic information

Entry
Database: PDB / ID: 4h5s
TitleComplex structure of Necl-2 and CRTAM
Components
  • Cell adhesion molecule 1
  • Cytotoxic and regulatory T-cell molecule
KeywordsCELL ADHESION / Ig fold / immune recognition
Function / homology
Function and homology information


detection of tumor cell / negative regulation of ERBB4 signaling pathway / regulation of CD8-positive, alpha-beta T cell activation / detection of stimulus / cell recognition / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / establishment of T cell polarity / lymphocyte migration into lymphoid organs / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...detection of tumor cell / negative regulation of ERBB4 signaling pathway / regulation of CD8-positive, alpha-beta T cell activation / detection of stimulus / cell recognition / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / establishment of T cell polarity / lymphocyte migration into lymphoid organs / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / Adherens junctions interactions / regulation of T cell activation / regulation of T cell differentiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / immune system process / negative regulation of activated T cell proliferation / homophilic cell adhesion via plasma membrane adhesion molecules / immunological synapse / cell adhesion molecule binding / negative regulation of protein phosphorylation / liver development / positive regulation of cytokine production / PDZ domain binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / cell-cell junction / spermatogenesis / basolateral plasma membrane / adaptive immune response / postsynaptic density / cell differentiation / neuron projection / signaling receptor binding / apoptotic process / synapse / dendrite / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytotoxic and regulatory T-cell molecule / Cell adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, S. / Lu, G. / Qi, J. / Li, Y. / Zhang, Z. / Zhang, B. / Yan, J. / Gao, G.F.
CitationJournal: Structure / Year: 2013
Title: Competition of cell adhesion and immune recognition: insights into the interaction between CRTAM and nectin-like 2.
Authors: Zhang, S. / Lu, G. / Qi, J. / Li, Y. / Zhang, Z. / Zhang, B. / Fan, Z. / Yan, J. / Gao, G.F.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Derived calculations
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytotoxic and regulatory T-cell molecule
B: Cell adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)22,8752
Polymers22,8752
Non-polymers00
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-8 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.042, 91.042, 56.684
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Cytotoxic and regulatory T-cell molecule / Class-I MHC-restricted T-cell-associated molecule


Mass: 11309.865 Da / Num. of mol.: 1 / Fragment: UNP residues 18-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRTAM / Production host: Escherichia coli (E. coli) / References: UniProt: O95727
#2: Protein Cell adhesion molecule 1 / Immunoglobulin superfamily member 4 / IgSF4 / Nectin-like protein 2 / NECL-2 / Spermatogenic ...Immunoglobulin superfamily member 4 / IgSF4 / Nectin-like protein 2 / NECL-2 / Spermatogenic immunoglobulin superfamily / SgIgSF / Synaptic cell adhesion molecule / SynCAM / Tumor suppressor in lung cancer 1 / TSLC-1


Mass: 11564.987 Da / Num. of mol.: 1 / Fragment: UNP residues 45-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CADM1, IGSF4, IGSF4A, NECL2, SYNCAM, TSLC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BY67
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O

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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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.15 M ammonium sulfate, 0.1 M Na-HEPES, and 20% PEG 4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 29635 / Num. obs: 29635 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.7→1.76 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.8 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8963 / SU ML: 0.16 / σ(F): 0 / Phase error: 17.36 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 1472 5.06 %Random
Rwork0.1654 ---
all0.1674 ---
obs0.1674 29094 98.19 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.993 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 67.71 Å2 / Biso mean: 21.2575 Å2 / Biso min: 5.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.6649 Å2-0 Å20 Å2
2---0.6649 Å20 Å2
3---1.3298 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 0 374 1933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061597
X-RAY DIFFRACTIONf_angle_d1.0952173
X-RAY DIFFRACTIONf_dihedral_angle_d13.461585
X-RAY DIFFRACTIONf_chiral_restr0.082263
X-RAY DIFFRACTIONf_plane_restr0.006275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6987-1.75350.26061430.2123240695
1.7535-1.81620.24481310.2006241895
1.8162-1.88890.24981320.1836243496
1.8889-1.97480.20251260.159247298
1.9748-2.07890.18381230.1546254599
2.0789-2.20910.19251400.15422525100
2.2091-2.37960.20681450.1641254399
2.3796-2.61890.19681390.1707252899
2.6189-2.99760.21781140.1684255399
2.9976-3.77550.20111600.15612553100
3.7755-29.80510.19821190.16242645100
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)
10.70890.2528-0.0870.1331-0.24431.22320.05290.2347-0.37620.1339-0.07790.1994-0.02750.3085-0.03790.1179-0.01410.020.1601-0.03480.22017.965415.6349-5.4034
20.73870.0657-0.01150.70240.23170.193-0.00970.2764-0.19810.26340.1242-0.07910.16270.1190.01660.1898-0.0155-0.04040.13350.01310.19045.194517.10932.8141
30.18620.05610.03250.2407-0.02520.0108-0.060.18530.0483-0.0808-0.0102-0.1773-0.08570.2637-0.05740.15830.0114-0.07520.1576-0.03380.176823.961530.48857.4207
40.4409-0.0501-0.09450.53610.02820.02550.0175-0.0731-0.07840.0180.0302-0.0167-0.0011-0.0683-0.00530.08430.00620.00030.1074-0.00160.09646.972930.92531.6344
50.51570.0007-0.15010.718-0.16080.0731-0.0349-0.34550.10660.24180.04390.36050.09310.04490.01320.12990.00040.02160.1938-0.0250.17311.872731.16718.4163
60.5306-0.0370.01640.2080.11460.06270.0349-0.1463-0.2290.17660.05390.0340.1194-0.0171-0.00140.1181-0.0131-0.04560.14540.01410.168110.446523.57799.5148
70.3986-0.5076-0.03050.67620.09220.15790.2520.06-0.0361-0.0789-0.240.1957-0.008-0.09040.01010.1089-0.02050.00790.1579-0.01340.1592-4.122319.4685-1.605
80.2051-0.0678-0.09210.40280.08350.19080.05280.0236-0.2462-0.0294-0.0019-0.28750.03820.0474-0.02540.07170.0072-0.00910.119-0.00360.108514.639930.2948-1.1647
90.28340.09960.00810.23150.05960.1486-0.06480.1185-0.17710.02560.01660.00950.01750.0182-0.03330.0761-0.00430.01880.1296-0.05920.15447.071620.4051-5.6771
100.2291-0.08-0.07640.44050.10930.23330.0713-0.00080.0804-0.1155-0.03830.0619-0.0335-0.0753-0.00510.0935-0.00070.02690.13430.00680.10127.255553.603-7.2034
110.33780.1284-0.11010.34190.04080.1770.0990.04450.0768-0.0354-0.03950.027-0.092-0.0152-0.00910.1137-0.01340.01850.1399-0.02090.08736.621452.7343-1.4731
120.48460.023-0.14870.53880.230.24210.02620.04850.17770.1487-0.24770.32090.1047-0.1878-0.0530.1235-0.04040.07140.1294-0.04060.1977-4.539646.88226.9987
130.3119-0.0374-0.00810.3120.05970.0150.02620.0561-0.05420.01140.00580.08550.0738-0.0125-0.01350.06830.00340.00990.0967-0.00550.074910.089141.1953-1.2541
140.22510.08910.09660.34140.09340.1616-0.0317-0.05610.05750.13150.0293-0.04170.03870.0943-0.03460.10530.0135-0.00210.1369-0.01680.083216.389743.82894.3842
150.2876-0.08010.03580.22520.09220.055-0.1231-0.1186-0.04960.08420.15480.081-0.02280.1372-0.0030.09750.00680.01220.1269-0.00580.077411.198151.63375.8245
160.25640.0157-0.1430.31740.09520.21420.06550.03380.0172-0.0511-0.01590.0023-0.12310.0397-0.01510.09140.010.01990.1186-0.00430.08113.781151.2024-3.4036
170.1654-0.2948-0.14520.51380.23350.10890.01030.1103-0.0453-0.0583-0.00870.04870.0246-0.0119-0.00850.05940.00010.00450.1056-0.00210.07165.38345.8586-6.731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:12)A5 - 12
2X-RAY DIFFRACTION2chain 'A' and (resseq 13:22)A13 - 22
3X-RAY DIFFRACTION3chain 'A' and (resseq 23:29)A23 - 29
4X-RAY DIFFRACTION4chain 'A' and (resseq 30:43)A30 - 43
5X-RAY DIFFRACTION5chain 'A' and (resseq 44:54)A44 - 54
6X-RAY DIFFRACTION6chain 'A' and (resseq 55:68)A55 - 68
7X-RAY DIFFRACTION7chain 'A' and (resseq 69:76)A69 - 76
8X-RAY DIFFRACTION8chain 'A' and (resseq 77:87)A77 - 87
9X-RAY DIFFRACTION9chain 'A' and (resseq 88:100)A88 - 100
10X-RAY DIFFRACTION10chain 'B' and (resseq 1:15)B1 - 15
11X-RAY DIFFRACTION11chain 'B' and (resseq 16:21)B16 - 21
12X-RAY DIFFRACTION12chain 'B' and (resseq 22:29)B22 - 29
13X-RAY DIFFRACTION13chain 'B' and (resseq 30:42)B30 - 42
14X-RAY DIFFRACTION14chain 'B' and (resseq 43:52)B43 - 52
15X-RAY DIFFRACTION15chain 'B' and (resseq 53:59)B53 - 59
16X-RAY DIFFRACTION16chain 'B' and (resseq 60:75)B60 - 75
17X-RAY DIFFRACTION17chain 'B' and (resseq 76:100)B76 - 100

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