[English] 日本語
Yorodumi
- PDB-6r0x: The extracellular domain of G6b-B in complex with Fab fragment an... -

+
Open data


ID or keywords:

Loading...

-
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 / platelet activation / blood coagulation / heparin binding ...megakaryocyte differentiation / platelet formation / megakaryocyte development / negative regulation of signal transduction / GPVI-mediated activation cascade / erythrocyte differentiation / integrin-mediated signaling pathway / platelet activation / blood coagulation / heparin binding / membrane => GO:0016020 / Golgi apparatus / endoplasmic reticulum / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more