[English] 日本語
Yorodumi
- PDB-6rlo: Crystal structure of AT1412dm Fab fragment in complex with CD9 la... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rlo
TitleCrystal structure of AT1412dm Fab fragment in complex with CD9 large extracellular loop
Components
  • (AT1412dm Fab Fragment ...) x 2
  • CD9 antigen
KeywordsIMMUNE SYSTEM / Antibody / Fab / CD9-binding / affinity-improvement
Function / homology
Function and homology information


Acrosome Reaction and Sperm:Oocyte Membrane Binding / myoblast fusion involved in skeletal muscle regeneration / sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / regulation of macrophage migration / paranodal junction assembly / glial cell migration / platelet alpha granule membrane / negative regulation of platelet aggregation / oligodendrocyte development ...Acrosome Reaction and Sperm:Oocyte Membrane Binding / myoblast fusion involved in skeletal muscle regeneration / sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / regulation of macrophage migration / paranodal junction assembly / glial cell migration / platelet alpha granule membrane / negative regulation of platelet aggregation / oligodendrocyte development / Uptake and function of diphtheria toxin / cellular response to low-density lipoprotein particle stimulus / clathrin-coated endocytic vesicle membrane / platelet activation / receptor internalization / integrin binding / endocytic vesicle membrane / Platelet degranulation / extracellular vesicle / cell population proliferation / cell adhesion / apical plasma membrane / negative regulation of cell population proliferation / external side of plasma membrane / focal adhesion / protein-containing complex / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
CD9, extracellular domain / Cd81 Antigen, Extracellular Domain; Chain: A / Tetraspanin / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Immunoglobulins ...CD9, extracellular domain / Cd81 Antigen, Extracellular Domain; Chain: A / Tetraspanin / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNeviani, V. / Pearce, N.M. / Pos, W. / Schotte, R. / Spits, H. / Gros, P.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research024.002.009 Netherlands
CitationJournal: To Be Published
Title: Structural basis of a homo-dimerization site in tetraspanin CD9 targeted by a melanoma patient-derived antibody
Authors: Neviani, V. / Pos, W. / Schotte, R. / Wagner, K. / Go, D.M. / Fatmawati, C. / Kedde, M. / Claassen, Y.B. / Kroon-Batenburg, L. / Lutz, M. / Verdegaal, E.M.E. / van der Burg, S.H. / Spits, H. / Gros, P.
History
DepositionMay 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AT1412dm Fab Fragment (Heavy Chain)
B: AT1412dm Fab Fragment (Light Chain)
I: CD9 antigen
C: AT1412dm Fab Fragment (Heavy Chain)
D: AT1412dm Fab Fragment (Light Chain)
J: CD9 antigen
E: AT1412dm Fab Fragment (Heavy Chain)
F: AT1412dm Fab Fragment (Light Chain)
K: CD9 antigen
G: AT1412dm Fab Fragment (Heavy Chain)
H: AT1412dm Fab Fragment (Light Chain)
L: CD9 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,99131
Polymers233,40112
Non-polymers59019
Water3,819212
1
A: AT1412dm Fab Fragment (Heavy Chain)
B: AT1412dm Fab Fragment (Light Chain)
I: CD9 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5549
Polymers58,3503
Non-polymers2046
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-101 kcal/mol
Surface area22250 Å2
MethodPISA
2
C: AT1412dm Fab Fragment (Heavy Chain)
D: AT1412dm Fab Fragment (Light Chain)
J: CD9 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,60712
Polymers58,3503
Non-polymers2579
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-134 kcal/mol
Surface area22310 Å2
MethodPISA
3
E: AT1412dm Fab Fragment (Heavy Chain)
F: AT1412dm Fab Fragment (Light Chain)
K: CD9 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4095
Polymers58,3503
Non-polymers582
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-62 kcal/mol
Surface area22330 Å2
MethodPISA
4
G: AT1412dm Fab Fragment (Heavy Chain)
H: AT1412dm Fab Fragment (Light Chain)
L: CD9 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4215
Polymers58,3503
Non-polymers712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-62 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.776, 89.858, 91.533
Angle α, β, γ (deg.)71.120, 89.590, 85.960
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17I
27J
18I
28K
19I
29L
110C
210E
111C
211G
112D
212F
113D
213H
114J
214K
115J
215L
116E
216G
117F
217H
118K
218L

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLYSLYSAA4 - 2294 - 221
21VALVALLYSLYSCD4 - 2294 - 221
12VALVALPROPROAA4 - 2284 - 220
22VALVALPROPROEG4 - 2284 - 220
13VALVALLYSLYSAA4 - 2294 - 221
23VALVALLYSLYSGJ4 - 2294 - 221
14ASPASPARGARGBB1 - 2271 - 217
24ASPASPARGARGDE1 - 2271 - 217
15ASPASPASNASNBB1 - 2261 - 216
25ASPASPASNASNFH1 - 2261 - 216
16ASPASPARGARGBB1 - 2271 - 217
26ASPASPARGARGHK1 - 2271 - 217
17LYSLYSPHEPHEIC114 - 1894 - 79
27LYSLYSPHEPHEJF114 - 1894 - 79
18LYSLYSASPASPIC114 - 1904 - 80
28LYSLYSASPASPKI114 - 1904 - 80
19LYSLYSPHEPHEIC114 - 1894 - 79
29LYSLYSPHEPHELL114 - 1894 - 79
110VALVALPROPROCD4 - 2284 - 220
210VALVALPROPROEG4 - 2284 - 220
111VALVALLYSLYSCD4 - 2294 - 221
211VALVALLYSLYSGJ4 - 2294 - 221
112ASPASPASNASNDE1 - 2261 - 216
212ASPASPASNASNFH1 - 2261 - 216
113ASPASPGLYGLYDE1 - 2281 - 218
213ASPASPGLYGLYHK1 - 2281 - 218
114LYSLYSPHEPHEJF114 - 1894 - 79
214LYSLYSPHEPHEKI114 - 1894 - 79
115LYSLYSASNASNJF114 - 1914 - 81
215LYSLYSASNASNLL114 - 1914 - 81
116VALVALGLUGLUEG4 - 2274 - 219
216VALVALGLUGLUGJ4 - 2274 - 219
117ASPASPASNASNFH1 - 2261 - 216
217ASPASPASNASNHK1 - 2261 - 216
118LYSLYSPHEPHEKI114 - 1894 - 79
218LYSLYSPHEPHELL114 - 1894 - 79

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

-
Components

-
Protein , 1 types, 4 molecules IJKL

#3: Protein
CD9 antigen / 5H9 antigen / Cell growth-inhibiting gene 2 protein / Leukocyte antigen MIC3 / Motility-related ...5H9 antigen / Cell growth-inhibiting gene 2 protein / Leukocyte antigen MIC3 / Motility-related protein / MRP-1 / Tetraspanin-29 / Tspan-29 / p24


Mass: 10260.629 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD9, MIC3, TSPAN29, GIG2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P21926

-
Antibody , 2 types, 8 molecules ACEGBDFH

#1: Antibody
AT1412dm Fab Fragment (Heavy Chain)


Mass: 23827.686 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
AT1412dm Fab Fragment (Light Chain)


Mass: 24261.814 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

-
Non-polymers , 4 types, 231 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: PEG 1000, sodium chloride, sodium potassium phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.96 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.2→84.8 Å / Num. obs: 104319 / % possible obs: 92.6 % / Redundancy: 3.9 % / CC1/2: 0.984 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.117 / Rrim(I) all: 0.231 / Net I/σ(I): 5 / Num. measured all: 406120 / Scaling rejects: 405
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.243.91.0482086253210.9820.6151.2161.394.6
12.05-84.83.60.04624186700.9990.030.05511.997.8

-
Processing

Software
NameVersionClassification
DIALSdata reduction
Aimless0.5.32data scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RLM

6rlm


Resolution: 2.2→84.8 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.88 / SU B: 11.105 / SU ML: 0.255 / SU R Cruickshank DPI: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.39 / ESU R Free: 0.264
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2866 5338 5.1 %RANDOM
Rwork0.2537 ---
obs0.2553 98939 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.31 Å2 / Biso mean: 29.944 Å2 / Biso min: 10.42 Å2
Baniso -1Baniso -2Baniso -3
1--2.62 Å2-0.09 Å20.84 Å2
2--2.94 Å2-1.19 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 2.2→84.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15644 0 19 212 15875
Biso mean--36.68 22.38 -
Num. residues----2027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01316028
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714378
X-RAY DIFFRACTIONr_angle_refined_deg1.341.64421790
X-RAY DIFFRACTIONr_angle_other_deg1.1451.57433573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8752011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66423.398727
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.439152606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1211560
X-RAY DIFFRACTIONr_chiral_restr0.050.22092
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217873
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023271
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A62880.05
12C62880.05
21A62400.06
22E62400.06
31A62400.06
32G62400.06
41B67080.04
42D67080.04
51B66050.05
52F66050.05
61B66990.05
62H66990.05
71I23310.07
72J23310.07
81I23030.09
82K23030.09
91I22960.07
92L22960.07
101C62190.06
102E62190.06
111C62230.06
112G62230.06
121D65930.06
122F65930.06
131D66910.05
132H66910.05
141J22910.07
142K22910.07
151J23580.07
152L23580.07
161E62300.06
162G62300.06
171F66480.04
172H66480.04
181K23210.06
182L23210.06
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 393 -
Rwork0.36 7422 -
all-7815 -
obs--94.44 %

+
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://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