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- PDB-5uv6: Crystal structure of human Opioid Binding Protein/Cell Adhesion M... -

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Basic information

Entry
Database: PDB / ID: 5uv6
TitleCrystal structure of human Opioid Binding Protein/Cell Adhesion Molecule Like (OPCML)
ComponentsOpioid-binding protein/cell adhesion molecule
KeywordsCELL ADHESION / GPI-anchored Ig domain Cell adhesion molecule
Function / homology
Function and homology information


neuron recognition / : / Post-translational modification: synthesis of GPI-anchored proteins / cell adhesion / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Opioid-binding protein/cell adhesion molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.65001977608 Å
AuthorsBirtley, J.R. / Stern, L.J. / Gabra, H. / Zanini, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH-AI038996 United States
CitationJournal: Nat Commun / Year: 2019
Title: Inactivating mutations and X-ray crystal structure of the tumor suppressor OPCML reveal cancer-associated functions.
Authors: Birtley, J.R. / Alomary, M. / Zanini, E. / Antony, J. / Maben, Z. / Weaver, G.C. / Von Arx, C. / Mura, M. / Marinho, A.T. / Lu, H. / Morecroft, E.V.N. / Karali, E. / Chayen, N.E. / Tate, E.W. ...Authors: Birtley, J.R. / Alomary, M. / Zanini, E. / Antony, J. / Maben, Z. / Weaver, G.C. / Von Arx, C. / Mura, M. / Marinho, A.T. / Lu, H. / Morecroft, E.V.N. / Karali, E. / Chayen, N.E. / Tate, E.W. / Jurewicz, M. / Stern, L.J. / Recchi, C. / Gabra, H.
History
DepositionFeb 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Opioid-binding protein/cell adhesion molecule
B: Opioid-binding protein/cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3098
Polymers63,2512
Non-polymers2,0586
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint23 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.564, 93.564, 262.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 43 through 61 or resid 63...A43 - 61
121(chain 'A' and (resid 43 through 61 or resid 63...A63 - 119
131(chain 'A' and (resid 43 through 61 or resid 63...A121 - 126
141(chain 'A' and (resid 43 through 61 or resid 63...A128 - 173
151(chain 'A' and (resid 43 through 61 or resid 63...A179 - 213
161(chain 'A' and (resid 43 through 61 or resid 63...A215 - 236
171(chain 'A' and (resid 43 through 61 or resid 63...A239 - 261
181(chain 'A' and (resid 43 through 61 or resid 63...A263 - 270
191(chain 'A' and (resid 43 through 61 or resid 63...A272
1101(chain 'A' and (resid 43 through 61 or resid 63...A274
1111(chain 'A' and (resid 43 through 61 or resid 63...A276 - 288
1121(chain 'A' and (resid 43 through 61 or resid 63...A290 - 319
211(chain 'B' and (resid 43 through 61 or resid 63...B43 - 61
221(chain 'B' and (resid 43 through 61 or resid 63...B63 - 119
231(chain 'B' and (resid 43 through 61 or resid 63...B121 - 126
241(chain 'B' and (resid 43 through 61 or resid 63...B128 - 173
251(chain 'B' and (resid 43 through 61 or resid 63...B179 - 213
261(chain 'B' and (resid 43 through 61 or resid 63...B215 - 236
271(chain 'B' and (resid 43 through 61 or resid 63...B239 - 261
281(chain 'B' and (resid 43 through 61 or resid 63...B263 - 270
291(chain 'B' and (resid 43 through 61 or resid 63...B272
2101(chain 'B' and (resid 43 through 61 or resid 63...B274
2111(chain 'B' and (resid 43 through 61 or resid 63...B276 - 288
2121(chain 'B' and (resid 43 through 61 or resid 63...B290 - 319

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Components

#1: Protein Opioid-binding protein/cell adhesion molecule / Opioid-binding cell adhesion molecule / IgLON family member 1


Mass: 31625.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OPCML, IGLON1, OBCAM / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14982
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: isolated from a natural 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 4.66 Å3/Da / Density % sol: 73.62 % / Description: Rectangular bipyramids.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: A 50/50 (v/v) mix of 1.6 M MgSO4, 0.1 M MES pH 6.5 with 20% PEG 8000, 100 mM HEPES pH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.65→18.5 Å / Num. obs: 34665 / % possible obs: 95.81 % / Redundancy: 14.4 % / Biso Wilson estimate: 62.8618429607 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.047 / Net I/σ(I): 9.71
Reflection shellResolution: 2.65→2.744 Å / Redundancy: 14.5 % / Rmerge(I) obs: 2.74 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3401 / CC1/2: 0.685 / Rpim(I) all: 0.74 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
iMOSFLM7.2.1data reduction
SCALA3.3.21data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.65001977608→18.4427015654 Å / SU ML: 0.530901192322 / Cross valid method: FREE R-VALUE / σ(F): 1.3269332535 / Phase error: 39.1522431261
RfactorNum. reflection% reflection
Rfree0.300280125102 1713 5.13304566703 %
Rwork0.284083141182 --
obs0.284949700167 33372 96.2006341885 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 84.6421742087 Å2
Refinement stepCycle: LAST / Resolution: 2.65001977608→18.4427015654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 134 40 4350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005810784819754400
X-RAY DIFFRACTIONf_angle_d0.8817336711186001
X-RAY DIFFRACTIONf_chiral_restr0.0538547637936732
X-RAY DIFFRACTIONf_plane_restr0.00472003162303753
X-RAY DIFFRACTIONf_dihedral_angle_d11.41878607432585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.72780.578843903951080.5061945047792323X-RAY DIFFRACTION86.728505173
2.7278-2.81550.4588534136021370.4210448719052674X-RAY DIFFRACTION98.4243697479
2.8155-2.91580.416546892441660.4179340602762640X-RAY DIFFRACTION99.2571630704
2.9158-3.0320.4213421187631500.3779369887282676X-RAY DIFFRACTION99.2972593113
3.032-3.16940.3582509149291390.3643483225762675X-RAY DIFFRACTION98.8061797753
3.1694-3.33550.3797387226431450.3406903275682676X-RAY DIFFRACTION98.6363636364
3.3355-3.54310.3051496466951380.3148101239192594X-RAY DIFFRACTION95.4577218728
3.5431-3.81450.3673384908141410.2901565079262621X-RAY DIFFRACTION96.0361613352
3.8145-4.19420.2611129061081430.2585972930882602X-RAY DIFFRACTION94.5573544609
4.1942-4.79180.2105677920251550.2231632841522639X-RAY DIFFRACTION95.8490566038
4.7918-6.00240.2590971744041490.2189384015462692X-RAY DIFFRACTION95.5279085407
6.0024-18.44310.2691684111491420.2479180632232847X-RAY DIFFRACTION95.8319974351
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)
19.27443693812.86135507484-0.6424182281584.77632898947-0.7528565912645.07488599537-0.5480626931130.592041016956-0.331153184248-0.8949892027060.163029655854-0.3346682069740.09566966501170.0693063032330.3113125682580.6848452036330.05299817713490.05519174266950.3467098360890.07776351459780.39284625665533.402342662627.0495556607296.183911639
26.88913403285-4.01274580863-7.254105214224.158035116472.978616148266.78403424609-0.447060141393-0.26442639217-0.1765936315310.857006143328-0.03870184274670.3177020807670.37080717119-0.3159900825750.528314811990.990455942937-0.1390882864960.2857095644770.948552160186-0.03071617618370.63910187884261.971399220912.3552217894259.511792058
31.577636392412.47884361961-1.18730182097.988685207981.439152495891.10706497302-0.463134499497-0.807162399197-1.80907059150.832030421873-0.323379299712-1.622254368770.7497492378370.6515699774590.562928787750.7232294659250.08656467028490.1213772102540.662966008890.3382675933171.0623757432788.6877442928-1.27601173233242.389681728
49.592132771594.3216702561-1.818469005687.255789766850.509569755166.59073465124-0.9696455431651.132210336190.249732957609-1.083902060320.4723915915730.3478651908320.149590833302-0.3753834254730.317678003110.658745960796-0.0181832937441-0.06963802484130.493098473226-0.09848774697670.42894865286212.544022841720.2693944131296.066317872
53.78179964282-2.503775808413.672801052883.2746059392-0.1884966149865.67654519123-0.430569767079-0.4338621194970.3091367600470.660162490595-0.0583910560872-0.813977650617-0.283355788720.6278250821110.4320867673981.0098715401-0.171927374235-0.4483442743481.341665932560.1029749496730.815011138714-10.228620608434.0188005854263.151626486
65.336115978310.9783583717453.118501916963.3254824549-0.4609483616112.69501646041-0.503096882715-0.8245920055221.324499554580.402603014691-0.2350399584270.486065352027-0.841841872884-0.4601104492770.5511489503630.7460520486230.0460176553276-0.1820881510480.602629513711-0.2153019072470.712552541971-42.820121492947.4399564884241.448527827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 133 )
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 241 )
3X-RAY DIFFRACTION3chain 'A' and (resid 242 through 319 )
4X-RAY DIFFRACTION4chain 'B' and (resid 43 through 133 )
5X-RAY DIFFRACTION5chain 'B' and (resid 134 through 221 )
6X-RAY DIFFRACTION6chain 'B' and (resid 222 through 319 )

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