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- PDB-6r0x: The extracellular domain of G6b-B in complex with Fab fragment an... -

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Basic information

Entry
Database: PDB / ID: 6r0x
TitleThe extracellular domain of G6b-B in complex with Fab fragment and DP12 heparin oligosaccharide.
Components
  • Megakaryocyte and platelet inhibitory receptor G6b
  • antibody fab fragment heavy chain
  • antibody fab fragment light chain
KeywordsBLOOD CLOTTING / platelets / signaling / ITIM-receptor / G6b-B / heparin
Function / homology
Function and homology information


megakaryocyte differentiation / platelet formation / megakaryocyte development / negative regulation of signal transduction / GPVI-mediated activation cascade / erythrocyte differentiation / integrin-mediated signaling pathway / blood coagulation / heparin binding / endoplasmic reticulum ...megakaryocyte differentiation / platelet formation / megakaryocyte development / negative regulation of signal transduction / GPVI-mediated activation cascade / erythrocyte differentiation / integrin-mediated signaling pathway / blood coagulation / heparin binding / endoplasmic reticulum / Golgi apparatus / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
G6B family / : / G6b-B extracellular V-set Ig-like domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Megakaryocyte and platelet inhibitory receptor G6b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.13 Å
AuthorsOgg, D.J. / McMiken, H.J. / Howard, T.D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
British Heart FoundationRG/15/13/31673 United Kingdom
British Heart FoundationFS/13/1/29894 United Kingdom
CitationJournal: Elife / Year: 2019
Title: Heparan sulfates are critical regulators of the inhibitory megakaryocyte-platelet receptor G6b-B.
Authors: Vogtle, T. / Sharma, S. / Mori, J. / Nagy, Z. / Semeniak, D. / Scandola, C. / Geer, M.J. / Smith, C.W. / Lane, J. / Pollack, S. / Lassila, R. / Jouppila, A. / Barr, A.J. / Ogg, D.J. / ...Authors: Vogtle, T. / Sharma, S. / Mori, J. / Nagy, Z. / Semeniak, D. / Scandola, C. / Geer, M.J. / Smith, C.W. / Lane, J. / Pollack, S. / Lassila, R. / Jouppila, A. / Barr, A.J. / Ogg, D.J. / Howard, T.D. / McMiken, H.J. / Warwicker, J. / Geh, C. / Rowlinson, R. / Abbott, W.M. / Eckly, A. / Schulze, H. / Wright, G.J. / Mazharian, A. / Futterer, K. / Rajesh, S. / Douglas, M.R. / Senis, Y.A.
History
DepositionMar 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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
A: antibody fab fragment heavy chain
B: antibody fab fragment light chain
C: antibody fab fragment heavy chain
D: antibody fab fragment light chain
E: Megakaryocyte and platelet inhibitory receptor G6b
F: Megakaryocyte and platelet inhibitory receptor G6b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,7159
Polymers128,0376
Non-polymers3,6773
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15400 Å2
ΔGint-31 kcal/mol
Surface area48430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.800, 72.340, 131.042
Angle α, β, γ (deg.)90.000, 124.520, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody antibody fab fragment heavy chain


Mass: 25761.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): embryonic / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Tissue (production host): kidney
#2: Antibody antibody fab fragment light chain


Mass: 25848.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Embryonic / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Tissue (production host): Kidney
#3: Protein Megakaryocyte and platelet inhibitory receptor G6b / Protein G6b


Mass: 12408.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The crystallography construct for G6b-B ECD contains the following point mutations to remove glycosylation sites; Asn32->Asp Ser67->Ala Ser68->Ala Ser69->Ala Thr71->Ala
Source: (gene. exp.) Homo sapiens (human) / Gene: MPIG6B, C6orf25, G6B, G6B-B / Cell (production host): embryonic / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Tissue (production host): kidney / References: UniProt: O95866
#4: Polysaccharide beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3[DNeup5Aca2-6]DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_a6-c2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 2327.897 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,8,7/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-AltpA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-AltpA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}}}}}LINUCSPDB-CARE
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: 56.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 50 mM MES pH6.2, 10% PEG 550MME, 5% v/v glycerol and 50 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 3.13→65.27 Å / Num. obs: 24543 / % possible obs: 97.3 % / Redundancy: 3 % / Biso Wilson estimate: 68.67 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.109 / Rrim(I) all: 0.193 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.13-3.33.11.21436090.4260.8171.46998.4
9.91-65.272.80.0377830.9950.0260.04691.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSJan 26, 2018data reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K2U

4k2u


Resolution: 3.13→63.1 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.847 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.46
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1153 4.7 %RANDOM
Rwork0.23 ---
obs0.232 24541 97.1 %-
Displacement parametersBiso max: 299.99 Å2 / Biso mean: 115.99 Å2 / Biso min: 48.32 Å2
Baniso -1Baniso -2Baniso -3
1--4.1025 Å20 Å2-19.1145 Å2
2---12.4772 Å20 Å2
3---16.5797 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: final / Resolution: 3.13→63.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7666 0 230 0 7896
Biso mean--158.95 --
Num. residues----1047
LS refinement shellResolution: 3.13→3.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2612 28 5.7 %
Rwork0.2287 463 -
all0.2304 491 -
obs--97.83 %
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)
11.21390.7643-2.20433.47883.31533.96890.0548-0.11410.2238-0.056-0.32980.7029-0.1092-0.29750.2750.27330.123-0.02780.3769-0.21680.084935.4615-7.577554.627
22.11660.2436-0.00214.32315.973610.4950.2653-0.17820.5604-0.3774-0.0290.1413-0.5441-0.107-0.23630.2031-0.18260.11790.0852-0.1017-0.000544.28317.585150.3197
35.5415-3.2538-4.11815.36253.81355.6798-0.0334-0.2960.0701-0.2250.3353-0.53740.04580.6345-0.30190.01580.00050.00350.2475-0.0602-0.177186.5821-67.688-20.0021
40.606-0.7316-0.67312.62320.99592.8298-0.518-0.4584-0.54750.13730.0801-0.20920.40530.73830.43790.42930.31330.07380.39330.33610.264580.3321-82.6206-12.5526
511.0781-1.5741-1.6914.80455.446214.58990.18560.27480.24330.180.0587-0.4773-0.14540.3772-0.24430.21170.0934-0.00410.078-0.1261-0.014747.7172-26.664915.7516
66.6585-2.3989-1.87579.98246.613713.398-0.4028-0.10260.15080.19420.2443-0.1701-0.0468-0.07780.15850.09220.1199-0.14780.1319-0.0873-0.039557.2437-46.00055.5315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|20 - A|238 }A20 - 238
2X-RAY DIFFRACTION2{ B|21 - B|234 }B21 - 234
3X-RAY DIFFRACTION3{ C|21 - C|240 }C21 - 240
4X-RAY DIFFRACTION4{ D|21 - D|234 }D21 - 234
5X-RAY DIFFRACTION5{ E|20 - E|1003 }E20 - 1003
6X-RAY DIFFRACTION6{ F|19 - F|1003 }F19 - 1003

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