3HSH | pdb_00003hsh

Crystal structure of human collagen XVIII trimerization domain (Tetragonal crystal form)

PDB DOI: https://doi.org/10.2210/pdb3HSH/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-06-10 Released: 2009-08-11
Deposition Author(s): Boudko, S.P., Bachinger, H.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.224 (Depositor), 0.226 (DCC)
R-Value Work:
0.175 (Depositor), 0.176 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of human collagen XVIII trimerization domain: A novel collagen trimerization Fold.

Boudko, S.P., Sasaki, T., Engel, J., Lerch, T.F., Nix, J., Chapman, M.S., Bachinger, H.P.

(2009) J Mol Biology 392: 787-802

PubMed: 19631658 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jmb.2009.07.057
Primary Citation Related Structures:
3HON, 3HSH

PubMed Abstract:
Collagens contain a unique triple-helical structure with a repeating sequence -G-X-Y-, where proline and hydroxyproline are major constituents in X and Y positions, respectively. Folding of the collagen triple helix requires trimerization domains. Once trimerized, collagen chains are correctly aligned and the folding of the triple helix proceeds in a zipper-like fashion. Here we report the isolation, characterization, and crystal structure of the trimerization domain of human type XVIII collagen, a member of the multiplexin family. This domain differs from all other known trimerization domains in other collagens and exhibits a high trimerization potential at picomolar concentrations. Strong chain association and high specificity of binding are needed for multiplexins, which are present at very low levels.

Organizational Affiliation

Research Department of Shriners Hospital for Children, Portland, OR 97239, USA.

Macromolecule Content

Total Structure Weight: 40.73 kDa
Atom Count: 3,184
Modeled Residue Count: 335
Deposited Residue Count: 336
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-1(XVIII) chain	A, B, C, D, E A, B, C, D, E, F	56	Homo sapiens	Mutation(s): 1 Gene Names: COL18A1
UniProt & NIH Common Fund Data Resources
Find proteins for P39060 (Homo sapiens) Explore P39060 Go to UniProtKB: P39060
PHAROS: P39060 GTEx: ENSG00000182871
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39060
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain G [auth A] SDF format, chain BA [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth F] mmCIF format, chain AA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth F]	AA [auth F] BA [auth F] G [auth A] H [auth A] I [auth A] AA [auth F], BA [auth F], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], U [auth C], V [auth C], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain W [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain T [auth B] SDF format, chain Q [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A] M [auth A] Q [auth B] R [auth B] S [auth B] L [auth A], M [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], W [auth C], Y [auth D], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.224 (Depositor), 0.226 (DCC)
R-Value Work: 0.175 (Depositor), 0.176 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.745	α = 90
b = 71.745	β = 90
c = 134.723	γ = 90

Software Package:

Software Name	Purpose
JBluIce-EPICS	data collection
Blu-Ice	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-08-11

Deposition Author(s):

Boudko, S.P.

Bachinger, H.P.

Revision History (Full details and data files)

Version 1.0: 2009-08-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2024-02-21
Changes: Data collection

3HSH | pdb_00003hsh

Crystal structure of human collagen XVIII trimerization domain (Tetragonal crystal form)

Literature

Crystal structure of human collagen XVIII trimerization domain: A novel collagen trimerization Fold.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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