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- PDB-5gmj: Crystal Structure of GRASP55 GRASP domain in complex with JAM-B C... -

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Basic information

Entry
Database: PDB / ID: 5gmj
TitleCrystal Structure of GRASP55 GRASP domain in complex with JAM-B C-terminus
Components
  • Golgi reassembly-stacking protein 2
  • Junctional adhesion molecule B
KeywordsSTRUCTURAL PROTEIN/PEPTIDE / beta strand sandswish / classic PDZ peptide binding groove / conserved carboxylate-binding loop / STRUCTURAL PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


positive regulation of lymphocyte migration / Golgi Cisternae Pericentriolar Stack Reorganization / lymphocyte aggregation / hematopoietic stem cell migration to bone marrow / cellular extravasation / establishment of protein localization to plasma membrane / organelle assembly / organelle organization / protein complex involved in cell adhesion / negative regulation of myelination ...positive regulation of lymphocyte migration / Golgi Cisternae Pericentriolar Stack Reorganization / lymphocyte aggregation / hematopoietic stem cell migration to bone marrow / cellular extravasation / establishment of protein localization to plasma membrane / organelle assembly / organelle organization / protein complex involved in cell adhesion / negative regulation of myelination / Integrin cell surface interactions / Cell surface interactions at the vascular wall / leukocyte tethering or rolling / cell-cell contact zone / myoblast fusion / negative regulation of cell adhesion / tight junction / Golgi organization / spermatid development / plasma membrane => GO:0005886 / Golgi medial cisterna / bicellular tight junction / somatodendritic compartment / response to endoplasmic reticulum stress / cell-cell adhesion / integrin binding / spermatogenesis / cell differentiation / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / cell surface / plasma membrane
Similarity search - Function
Junctional adhesion molecule B / GRASP55/65 / GRASP-type PDZ domain / GRASP55/65 PDZ-like domain / GRASP-type PDZ domain profile. / PDZ domain / Pdz3 Domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type ...Junctional adhesion molecule B / GRASP55/65 / GRASP-type PDZ domain / GRASP55/65 PDZ-like domain / GRASP-type PDZ domain profile. / PDZ domain / Pdz3 Domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / PDZ superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Golgi reassembly-stacking protein 2 / Junctional adhesion molecule B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.986 Å
AuthorsShi, N. / Shi, X. / Morelli, X. / Betzi, S. / Huang, X.
Funding support China, France, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370738 China
Campus FrancePHC CAI YUANPEI 2013 - Project N26203WD France
CitationJournal: PLoS Genet. / Year: 2017
Title: Genetic, structural, and chemical insights into the dual function of GRASP55 in germ cell Golgi remodeling and JAM-C polarized localization during spermatogenesis
Authors: Cartier-Michaud, A. / Bailly, A.L. / Betzi, S. / Shi, X. / Lissitzky, J.C. / Zarubica, A. / Serge, A. / Roche, P. / Lugari, A. / Hamon, V. / Bardin, F. / Derviaux, C. / Lembo, F. / Audebert, ...Authors: Cartier-Michaud, A. / Bailly, A.L. / Betzi, S. / Shi, X. / Lissitzky, J.C. / Zarubica, A. / Serge, A. / Roche, P. / Lugari, A. / Hamon, V. / Bardin, F. / Derviaux, C. / Lembo, F. / Audebert, S. / Marchetto, S. / Durand, B. / Borg, J.P. / Shi, N. / Morelli, X. / Aurrand-Lions, M.
History
DepositionJul 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Golgi reassembly-stacking protein 2
B: Golgi reassembly-stacking protein 2
C: Junctional adhesion molecule B
D: Junctional adhesion molecule B


Theoretical massNumber of molelcules
Total (without water)56,3254
Polymers56,3254
Non-polymers00
Water59433
1
A: Golgi reassembly-stacking protein 2
B: Golgi reassembly-stacking protein 2
C: Junctional adhesion molecule B
D: Junctional adhesion molecule B

A: Golgi reassembly-stacking protein 2
B: Golgi reassembly-stacking protein 2
C: Junctional adhesion molecule B
D: Junctional adhesion molecule B


Theoretical massNumber of molelcules
Total (without water)112,6508
Polymers112,6508
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area19820 Å2
ΔGint-99 kcal/mol
Surface area34590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.989, 132.989, 219.397
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: GLU / End label comp-ID: GLU

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SERSERchain AAA-14 - 20813 - 235
2GLUGLUchain BBB-15 - 20812 - 235

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Components

#1: Protein Golgi reassembly-stacking protein 2 / GRS2 / Golgi reassembly-stacking protein of 55 kDa / GRASP55


Mass: 25945.014 Da / Num. of mol.: 2 / Fragment: grasp domain, UNP residues 2-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gorasp2,GOLPH6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99JX3
#2: Protein/peptide Junctional adhesion molecule B / JAM-B / Junctional adhesion molecule 2 / JAM-2 / Vascular endothelial junction-associated molecule / VE-JAM


Mass: 2217.540 Da / Num. of mol.: 2 / Fragment: peptide of JamB C termianl / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9JI59
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 4.31 Å3/Da / Density % sol: 74.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: sodium formate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.986→54.85 Å / Num. obs: 20363 / % possible obs: 99.93 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.1792 / Net I/σ(I): 11.66
Reflection shellResolution: 2.986→3.093 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 4.14 / % possible all: 99.85

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RLE

3rle


Resolution: 2.986→54.849 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2739 1875 9.83 %Random selection
Rwork0.2247 34410 --
obs0.2296 19080 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.19 Å2 / Biso mean: 69.8719 Å2 / Biso min: 24.15 Å2
Refinement stepCycle: final / Resolution: 2.986→54.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 0 33 3587
Biso mean---53.35 -
Num. residues----461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053659
X-RAY DIFFRACTIONf_angle_d1.1654961
X-RAY DIFFRACTIONf_chiral_restr0.044544
X-RAY DIFFRACTIONf_plane_restr0.006648
X-RAY DIFFRACTIONf_dihedral_angle_d12.8211342
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1948X-RAY DIFFRACTION13.141TORSIONAL
12B1948X-RAY DIFFRACTION13.141TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9864-3.02420.33611360.279412931429100
3.0242-3.0640.36221350.26712611396100
3.064-3.1060.38711370.263612771414100
3.106-3.15040.27781450.259612751420100
3.1504-3.19740.32511460.232912831429100
3.1974-3.24730.26531370.23912681405100
3.2473-3.30060.27681390.230912951434100
3.3006-3.35750.29661400.246512611401100
3.3575-3.41850.32511340.223112731407100
3.4185-3.48430.25481400.228212801420100
3.4843-3.55540.26981380.232412541392100
3.5554-3.63270.25611400.20912751415100
3.6327-3.71710.23641390.206712791418100
3.7171-3.81010.30651380.216412831421100
3.8101-3.91310.27821350.211912701405100
3.9131-4.02820.2581390.216812871426100
4.0282-4.15820.28211400.201512751415100
4.1582-4.30670.2921350.201212721407100
4.3067-4.47910.23621370.194112671404100
4.4791-4.68280.20551380.194312771415100
4.6828-4.92960.26221380.200512811419100
4.9296-5.23820.26181410.203612641405100
5.2382-5.64230.29331390.240712631402100
5.6423-6.20940.3121390.249512811420100
6.2094-7.10620.30211390.24512771416100
7.1062-8.94680.23181400.248412791419100
8.9468-54.85850.27141460.24721260140699
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)
14.18513.4608-2.47493.7467-1.13672.3967-0.59681.89111.3301-0.31340.92371.1366-0.2297-0.613-0.48580.4031-0.157-0.0920.52240.18410.612953.983212.045213.6436
24.0768-0.3897-1.02367.2621-4.00397.7182-0.04730.3092-0.0489-0.23120.33270.1268-0.364-0.4274-0.26430.5646-0.2171-0.12320.51280.1620.38379.190924.4570.0665
35.61952.6271-3.17552.0767-1.9172.11320.17650.04330.27680.0442-0.0571-0.0238-0.5401-0.0786-0.19230.6346-0.2134-0.05370.4490.21760.478282.437529.95760.7504
40.65291.30280.07135.3720.35592.03410.0977-0.1437-0.3744-0.3495-0.1214-0.08860.3951-0.42310.08530.4667-0.4445-0.18220.55960.10920.455184.191620.561-0.8062
57.01221.4327-0.38455.15110.16673.2611-0.69630.29320.4473-0.60210.329-0.14160.2072-0.0039-0.06010.4897-0.29210.15160.4144-0.06360.374777.23830.47717.4578
67.70381.0882-2.790.9279-0.16971.0757-0.17171.46470.4624-0.97210.00360.45390.5922-0.3971-0.23561.9819-0.5242-0.20821.4291-0.10450.646174.4911.3922-8.2789
75.08980.6798-0.19614.4365-1.44891.9906-0.41590.56860.0307-0.59220.1072-0.67930.054-0.07550.29750.5647-0.27460.05770.50160.03180.306176.32324.88146.8576
85.88233.74471.69116.81092.27973.82140.3901-0.4789-0.95210.743-0.4368-1.02270.62990.28980.29130.5513-0.0244-0.06940.30890.02690.487776.9016-14.119219.7514
97.59741.14221.1854.96190.24213.04230.04720.3276-1.30180.044-0.1721-0.95491.0690.623-0.02970.52780.0878-0.08580.4960.04070.600389.549210.615532.5996
107.42850.43352.6624.19951.35085.80950.0619-0.3286-0.36430.2620.1433-0.12390.0895-0.116-0.19060.3274-0.0017-0.11870.38690.04110.311792.851115.540332.9826
115.851-1.34270.73624.31221.09071.1852-0.0581-0.74830.30420.6503-0.0479-0.01960.0581-0.02140.04030.5002-0.133-0.07550.4010.00820.221669.31329.766429.6468
124.9884-1.33743.23870.3923-0.84682.1161-0.0079-2.2296-0.63770.74510.08630.9863-0.0303-0.9432-0.1070.7064-0.0380.05540.86520.13560.513382.758115.501441.2678
132.8426-2.177-0.48594.5014-3.86386.41391.0439-0.661-0.0177-0.7984-2.08831.2431.0789-0.22180.39770.9956-0.3119-0.09560.81-0.16090.688284.476616.8453-6.6187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -14 through 5 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 53 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 85 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 109 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 110 through 139 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 140 through 160 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 161 through 208 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid -15 through 4 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 26 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 27 through 110 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 111 through 208 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 12 through 19 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 14 through 19 )D0

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