[English] 日本語
Yorodumi
- PDB-4lmq: Development and Preclinical Characterization of a Humanized Antib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lmq
TitleDevelopment and Preclinical Characterization of a Humanized Antibody Targeting CXCL12
Components
  • Stromal cell-derived factor 1
  • hu30D8 Fab heavy chain
  • hu30D8 Fab light chain
Keywordscell adhesion/immune system / immunoglobulin / cell adhesion-immune system complex
Function / homology
Function and homology information


chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance ...chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of dopamine secretion / Signaling by ROBO receptors / induction of positive chemotaxis / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / chemokine-mediated signaling pathway / blood circulation / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / positive regulation of calcium ion import / detection of temperature stimulus involved in sensory perception of pain / positive regulation of cell adhesion / positive regulation of T cell migration / animal organ regeneration / Nuclear signaling by ERBB4 / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / cell chemotaxis / adult locomotory behavior / axon guidance / neuron migration / response to virus / growth factor activity / defense response / intracellular calcium ion homeostasis / response to peptide hormone / chemotaxis / integrin binding / G alpha (i) signalling events / collagen-containing extracellular matrix / Estrogen-dependent gene expression / response to hypoxia / cell adhesion / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / signal transduction / extracellular exosome / extracellular region
Similarity search - Function
CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulins / Immunoglobulin-like ...CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Stromal cell-derived factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.773 Å
AuthorsZhong, Z. / Wang, J. / Li, B. / Xiang, H. / Ultsch, M. / Coons, M. / Wong, T. / Chiang, N.Y. / Clark, S. / Clark, R. ...Zhong, Z. / Wang, J. / Li, B. / Xiang, H. / Ultsch, M. / Coons, M. / Wong, T. / Chiang, N.Y. / Clark, S. / Clark, R. / Quintana, L. / Gribling, P. / Suto, E. / Barck, K. / Corpuz, R. / Yao, J. / Takkar, R. / Lee, W.P. / Damico-Beyer, L.A. / Carano, R.D. / Adams, C. / Kelley, R.F. / Wang, W. / Ferrara, N.
CitationJournal: Clin.Cancer Res. / Year: 2013
Title: Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12.
Authors: Zhong, C. / Wang, J. / Li, B. / Xiang, H. / Ultsch, M. / Coons, M. / Wong, T. / Chiang, N.Y. / Clark, S. / Clark, R. / Quintana, L. / Gribling, P. / Suto, E. / Barck, K. / Corpuz, R. / Yao, ...Authors: Zhong, C. / Wang, J. / Li, B. / Xiang, H. / Ultsch, M. / Coons, M. / Wong, T. / Chiang, N.Y. / Clark, S. / Clark, R. / Quintana, L. / Gribling, P. / Suto, E. / Barck, K. / Corpuz, R. / Yao, J. / Takkar, R. / Lee, W.P. / Damico-Beyer, L.A. / Carano, R.D. / Adams, C. / Kelley, R.F. / Wang, W. / Ferrara, N.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 27, 2021Group: Database references / Structure summary / Category: database_2 / entity / entity_name_com
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_fragment

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Stromal cell-derived factor 1
E: hu30D8 Fab heavy chain
F: Stromal cell-derived factor 1
H: hu30D8 Fab heavy chain
I: hu30D8 Fab light chain
L: hu30D8 Fab light chain


Theoretical massNumber of molelcules
Total (without water)108,2126
Polymers108,2126
Non-polymers00
Water1,06359
1
D: Stromal cell-derived factor 1
H: hu30D8 Fab heavy chain
L: hu30D8 Fab light chain


Theoretical massNumber of molelcules
Total (without water)54,1063
Polymers54,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: hu30D8 Fab heavy chain
F: Stromal cell-derived factor 1
I: hu30D8 Fab light chain


Theoretical massNumber of molelcules
Total (without water)54,1063
Polymers54,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.949, 73.101, 106.626
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number4
Space group name H-MP1211
Detailsantibody-antigen complex

-
Components

#1: Protein Stromal cell-derived factor 1 / / SDF-1 / hSDF-1 / C-X-C motif chemokine 12 / Intercrine reduced in hepatomas / IRH / hIRH / Pre-B ...SDF-1 / hSDF-1 / C-X-C motif chemokine 12 / Intercrine reduced in hepatomas / IRH / hIRH / Pre-B cell growth-stimulating factor / PBSF / SDF-1-beta(3-72) / SDF-1-alpha(3-67)


Mass: 7202.547 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 29-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1, SDF1A, SDF1B / Production host: Escherichia coli (E. coli) / References: UniProt: P48061
#2: Antibody hu30D8 Fab heavy chain


Mass: 23370.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody hu30D8 Fab light chain


Mass: 23533.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1, SDF1A, SDF1B / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M NaF, 0.1M Bis-tris, propane, 23%w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.95369 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2012
RadiationMonochromator: Curved Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.77→73 Å / Num. all: 25573 / Num. obs: 25088 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.77→2.78 Å / % possible all: 87.9

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.773→55.296 Å / SU ML: 0.49 / σ(F): 1.11 / Phase error: 32.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3007 2351 5.02 %
Rwork0.2527 --
obs0.255 25067 94.2 %
all-25573 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.616 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.1715 Å2-0 Å2-14.1637 Å2
2---0.4526 Å20 Å2
3---6.5537 Å2
Refinement stepCycle: LAST / Resolution: 2.773→55.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7339 0 0 59 7398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037519
X-RAY DIFFRACTIONf_angle_d0.71710196
X-RAY DIFFRACTIONf_dihedral_angle_d14.4142702
X-RAY DIFFRACTIONf_chiral_restr0.0561149
X-RAY DIFFRACTIONf_plane_restr0.0061297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7732-2.82980.38971260.3592671X-RAY DIFFRACTION94
2.8298-2.89130.39741480.34462594X-RAY DIFFRACTION95
2.8913-2.95860.34151240.33322684X-RAY DIFFRACTION94
2.9586-3.03260.36661480.31812512X-RAY DIFFRACTION93
3.0326-3.11460.38221230.33132579X-RAY DIFFRACTION93
3.1146-3.20620.35491590.30362648X-RAY DIFFRACTION96
3.2062-3.30970.32321220.29772667X-RAY DIFFRACTION95
3.3097-3.4280.32631250.28172645X-RAY DIFFRACTION95
3.428-3.56520.341500.27352593X-RAY DIFFRACTION94
3.5652-3.72740.34671350.2512624X-RAY DIFFRACTION94
3.7274-3.92390.35871360.24372629X-RAY DIFFRACTION93
3.9239-4.16960.29341450.22852524X-RAY DIFFRACTION92
4.1696-4.49140.25381250.1962628X-RAY DIFFRACTION95
4.4914-4.94320.23421380.17822684X-RAY DIFFRACTION95
4.9432-5.65790.27281410.2152587X-RAY DIFFRACTION93
5.6579-7.12590.25471480.25432607X-RAY DIFFRACTION94
7.1259-55.30750.22251580.21582622X-RAY DIFFRACTION95
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)
10.0138-0.0346-0.0060.0931-0.0370.09270.02550.02610.0396-0.11020.0371-0.0140.0526-0.00740.13310.0347-0.07990.0572-0.05150.05280.04275.8347-5.285741.6541
20.0131-0.0091-0.00140.0386-0.01250.0248-0.02790.0150.0271-0.0538-0.02970.0324-0.1022-0.0619-0.09020.19740.0218-0.11540.14090.0430.1078-22.28270.255923.3307
30.0793-0.0144-0.01330.02450.00380.0973-0.0724-0.0451-0.0932-0.014-0.0506-0.05010.05150.0287-0.172-0.0051-0.02630.06050.03420.04410.095554.2161-0.941780.9387
40.0724-0.0293-0.02280.0273-0.00740.02120.0242-0.04480.06240.04610.1010.0454-0.00280.07480.00720.50370.0831-0.02170.53480.14460.227770.5552-4.5507110.2947
50.02160.0055-0.01420.0048-0.00620.0122-0.01140.0131-0.0269-0.0162-0.0132-0.04790.02370.015-0.01870.0359-0.0267-0.01630.01830.02180.064234.8567-7.776656.8481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:117 ) OR ( CHAIN L AND RESID 1:110 )H1 - 117
2X-RAY DIFFRACTION1( CHAIN H AND RESID 1:117 ) OR ( CHAIN L AND RESID 1:110 )L1 - 110
3X-RAY DIFFRACTION2( CHAIN H AND RESID 118:213 ) OR ( CHAIN L AND RESID 111:214 )H118 - 213
4X-RAY DIFFRACTION2( CHAIN H AND RESID 118:213 ) OR ( CHAIN L AND RESID 111:214 )L111 - 214
5X-RAY DIFFRACTION3( CHAIN I AND RESID 1:110 ) OR ( CHAIN E AND RESID 1:115 )I1 - 110
6X-RAY DIFFRACTION3( CHAIN I AND RESID 1:110 ) OR ( CHAIN E AND RESID 1:115 )E1 - 115
7X-RAY DIFFRACTION4( CHAIN I AND RESID 111:214 ) OR ( CHAIN E AND RESID 118:213 )I111 - 214
8X-RAY DIFFRACTION4( CHAIN I AND RESID 111:214 ) OR ( CHAIN E AND RESID 118:213 )E118 - 213
9X-RAY DIFFRACTION5( CHAIN D AND RESID 11:68 )D11 - 68

+
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